Cast into two-deep water and the bobber will often glitch to one block above the surface of the water. Other casts may cause the bobber to glitch between 1 meter under water and the surface. In this case it still produces bubbles as it moves.
The bobber's up-and-down movement is very similar, possibly identical to what you sometimes see when villagers and other mobs sink into the ground, except here you have a floating item rather than a sinking one and it never turns black. It's /not/ the same as the bobber's normal movement, which may or may not be superimposed on top of the glitchy behaviour. I've experienced the problem with sinking mobs for some time now (not seen yet in latest build however), but this bobber behaviour is completely new to me.
BTW, this behaviour begins /after/ you've cast the line.
The height of the bobber depends on the where the player aims when casting the rod. Looking down the bobber is above the water, looking up the bobber is below the water, the bobber is on the surface if the player looks directly horizontal. (1.9-pre2)
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Confirmed in 1.5.1. The line must be cast extremely close to the player to reproduce this.
Added an animated GIF image of this bug occurring.
The first two frames are of casting while stationary, the next three are taken while walking into the river.
Does not neccessarily occur when close to the player. The line is also stuck when the bobber bounces of the edge of a solid block before it hits the water. Then it happens then no matter what the distance is. At least you can still catch fish from the air there. 😃
It seems that casting while standing on half block (being at a half height elevation) can also cause this. (or might be the cause)
I've seen this while standing on perfectly ordinary blocks. It's way more obvious when you're fishing up close, and makes fishing look very odd then. However, on examination, this seems to be usual behavior. Possibly meant to make the bobber visible? Still weird that it can't just be on the surface of the water, even if that makes it less visible when "dipping". Also, confirming for 1.5.2. (ETA: also for Ubuntu.)
happend to me in 1.6.2 too

Saw this today while playing!
Confirmed in 13w36a
Also in 13w36b.
It's not two deep water that causes it, its casting it close to you that causes it. (In 13w36b at least)
This may be an unrelated issue, but sometimes when fishing close to you and this glitch happens, you catch no fish. May be client/server desync. Seen on 13w36a/b.

... affects 13w37b !
the know giving fish happen to me i miss three fish from it i hope they fix all of these bugs/glitches
It happened to me today after I pressed F5 several times. Don't know if it was coincidence or not.
confirm in 13w39b
confirm in 13w41a
confirm in 13w41b
confirm 1.7.2
I think I have a good idea of what one of the factors is to cause this. As people have mentioned, the effect is more apparent the closer you cast to yourself. I'm fairly certain that it has to do with the code that causes the Lure to raise to the surface.
I'm not familiar with the code, but it looks like the game tries to raise Lure by twice the depth that it sinks when you cast it initially. This is a negligible amount when you cast a great distance away, as most of the force is directed horizontally rather than down, so the Lure doesn't go as far below the surface.
But when you cast from right off the edge of a block and look straight down, the Lure goes about 2 blocks underwater before rising 2 blocks above the water. So I think the code for deciding how deep the Lure went is the culprit.
Edit: Further evidence of this is if you go underwater and cast your Fishing Rod straight upwards. It will raise upwards about 2 blocks, then settle about 2 blocks below the surface, so it looks like in that case the game thinks it went 2 blocks above the surface and compensates by lowering it, while hitting the bug that double the number of blocks it should correct it by.
confirm 1.7.3/1.7.4
This happens to me all the time! Hopefully, Mojang will notice this and fix it... It's really annoying me.
I'm going to test this in Creative mode and see if it happens while flying too.
Yes, it does it when flying.
confirmed in 14w04b.
This issue reminds me of an issue I had with Computercraft: I would add one to the variable (x = x+1) whenever I went up but I forgot to subtract one whenever I went down. Maybe when the bobber hits a block while being cast, it still subtracts one from it's height value, even though it's not going down and then comes up too far because of the variable information. I really want this bug fixed as fishing is one of, if not the best, ways to get food early game.
Perhaps you could add a test to fix this: In Computercraft, turtle.forward() ATTEMPTS to move the turtle forward and if it succeeds, it returns true, but if it doesn't move, it returns false. So...
if turtle.forward() true then
x=x+1
end
Maybe you could do something like this or better with the fishing rod bobber and the water level:
while bobberLevel < 0 do //while the bobber is below the water do the following
if bobberLevel < (variable for tracking bobber movement using co-ordinates) then //if the bobber is less than it's it's previously recorded position then...
(move graphical bobber down)
end
end
I'm pretty sure an experienced programmer would know how to check the XYZ of the bobber and move move the graphic in a better way than 3 if statements inside a while loop.
Sometimes if you let a fish bite and get away, the game will realize this bug and fix itself... But you might as well catch that fish instead of letting it get away unless you're recording video footage or something similar.
It turns out, the bobber is not always hitting a block when it bugs out: it also does this when thrown in the water when facing an angle > 35, 40 or 55 depending if the block you are casting is level with the water, a block above, or two blocks above the water line respectively. (Thanks new debug screen) Bug angle trend stops at 3 blocks above the water where you can cast at any angle without bugs in 2 block deep or more water.
Temporary fix:
Fish 3 or more blocks above the water line for almost bugless fishing. Just make sure the first 3 blocks away from your fishing platform are at least 2 deep.
Fish 4 blocks above the water line for bugless fishing at any angle and any depth.
At any height, make sure not to hit a block before you hit the water. ex, cast> hits block> slides into the water and does glitch
Can still reproduce in 14w10c.
Still exists in 14w10c.
Confirmed for 14w11b
Still exists in 14w17a
Confirmed in 14w21b
Confirmed for 14w29a and b.
still exist in the newest version 1.7.10
and btw, if you stand in a higher ground(3 blocks higher than the water you are gonna fish) and cast a line in water, it will show as normal. thats the only way i know for now for how to fish normally in these version
Wait this is considered a bug? I thought this was an intentional change to stop people from having infinite fishing rods (pointing straight down into a well so that the bobber never hits anything but water). There was some auto-fishing trick where you pointed straight down in a well and put a book on the button. The fact that catching a fish in 1 second was possible pre-1.7 meant every 1 out of 1000 times it would catch something. And the durability never went down if the bobber didn't hit anything solid (I'm pretty sure they changed that in 1.7 too).
it happens when aiming the rod down about 45º
This also happens with several versions of Windows including the most recent version 1.8.3. It is very frustrating. This glitch didn't happen when I first purchased the game, and it devalues the game significantly in my mind and makes fishing even more difficult particularly when it is raining. I wish this would get fixed especially since it was an earlier update that created this problem.
In 1.8.7
It very much has to do with the angle, both facing and pitch. Facing near the diagonals will require you to have a very shallow pitch in order to get a successful cast (around 13º or lower when facing exactly 45º). Facing near the cardinal directions will require you to have a very steep pitch in order to cause a glitched cast. These numbers are for when the water and land is at the same height.
affects 15w31a and 15w32c
Jonathan seems to be right; I have experienced this in 1.8.7, and it seems consistently to happen if I cast downwards. Casting upwards doesn't seem to cause this problem (although it so happens that casting upwards results in it being far from the player and downwards close with the elevation of the water I was fishing in [same height as land], so it could be distance).
I have this problem in 1.8.8. It usually happens casting downwards.
I am still getting this in Windows, snapshot 15w38b.
Affects 15w44b
Confirmed for 15w47a and 15w47c
Confirmed for 15w51b
This issue relates to MC-94169
Confirmed for 16w05b
Confirmed for 16w07a
Confirmed for 1.9-pre2
The height of the bobber depends on the where the player aims when casting the rod. Looking down the bobber is above the water, looking up the bobber is below the water, the bobber is on the surface if the player looks directly horizontal. (1.9-pre2)
as of 1.9-pre2, the bobber now hovers above the waterline farther out than before – i.e. now I have to cast much further out for the appearance of the bobber to look as though it is resting on the water, making it less practical/easy at that distance to watch for when a fish is about to bite.
Still happens in 1.9-pre3.
also of note, possibly related, is the fact that once cast, the fishing line at the players end, does not connect to the end of the pole but is spaced off to the right floating in the air next to the pole end.
Just seen this in 1.9. The fishing line remains visible after catching something. See the two screenshots.
32 bit windows 7, survival, vanilla Minecraft.
Confirmed for 1.9.1-pre3.
Confirmed for 1.9.3-pre3.
Still in 1.9.4
Confirmed for 16w20a.
Still in 16w21a and 16w21b
Still in 1.10-pre1
Confirmed for 1.10-pre2.
Confirmed for 1.10.
Confirmed for 1.10.1.
Confirmed for 1.10.2
Confirmed in 16w32a
Confirmed in 16w32b
Confirmed in 16w33a
Still in 16w35a.
Confirmed in 16w36a
Still in 16w38a.
Confirmed in 16w39a
Confirmed in 16w39b
Confirmed in 16w39c
Confirmed in 16w40a
Still in 16w41a.
Still in 16w42a.
I was about to make a bug report about it until i found this, apparently the bob only floats if you cast it into water right in front of you, but if you cast it farther out, it wont float. This is probably the most annoying bug when fishing.