I killed the ender dragon and got my first end portal, however the 2nd and 3rd times I killed her another gateway did not spawn.
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Ok, now I can reproduce this issue TWICE. This happens when you defeated the 2nd ender dragon in the world that been upgraded from 1.19.3 to 1.19.4. Here is the "Steps to Reproduce":
Step 1: Create the world in 1.19.3
Step 2: Enter the End
Step 3: Use the command "/kill @e[type=ender_dragon]" to kill the ender dragon -> Notice that the end gateway spawn
Step 4: Exit the world and upgrade this world to 1.19.4
Step 5: Join that world and summon the ender dragon using end crystals
Step 6: Wait until the ender dragon show up
Step 7: Again use the command "/kill @e[type=ender_dragon]" to kill the ender dragon -> Notice that NO end gateway spawn

thanks @Brain81505, now i can reproduce this issue

This has nothing to do with a supposed world update. End gateways (the second and subsequent) for some reason don't seem to spawn if you exit the game before killing the dragon. The time the dragon gets re-summoned doesn't seem to matter, i.e. it doesn't make a difference if you place the end crystal before exiting the game.
This isn't an issue in 1.19.3.

I also have this issue on my realm, I did kill the dragon without leaving the game. The realm updated from 1.19.3 to 1.19.4 like 1.5 weeks ago.

My world was created in this snapshot (23w07a), I didn't update it to a new version.

Similar Bug but the cause might be slightly different.
1.19.4 Realm (start date 3/28/2023)
The Realm was started in 1.19.4
The group of us were killing the dragon together. Everyone hit the dragon at least once (probably).
Player A hit the dragon.
Player A got killed by an enderman
We keep attacking dragon
Player B hit and killed the dragon
Player A is at his spawn in the overworld... game gives Player A the credit for dragon kill
Game spawns one gateway.
The next Day.
Players C and B respawn and kill the dragon
No gateway
Player B logged off
Player C kills dragon and gateway spawns
Player C kills more dragons (6 total gateways)
The next day
Players B and C kill the dragon twice with no Gateways
Player B logs off
Player C kills dragon
No gateway
Player A is the realm owner.
Player C is me.

First part is MC-260903.

Affects 23w12a and 23w13a

I am having the same issue.
My world started on Java 1.19.4
I am running Fedeora Linux running Open Java 17.0.3 64 bit.
My cpu is an AMD R5 3600.
My video card is NVIDIA Geforce RTX 2070 Super.
I have increased the ram from 2Gb to 4Gb in the launcher. I have also disabled the F3 screen in the create world menu. Other than that, everything is vanilla.
I get the feeling that it is just creating the second portal over the first. Unfortunately, it goes to the same island as the first one.
I should add that I tried killing the dragon with beds the first time. So there is an obsidian block 1 block off the center and 1 block up from the post of the dragons perch.
[Edit]
I have decided to remove the obsidian block by the perch. Gave my self 4 end crystals, summoned the dragon, and used the kill command to kill the dragon, /kill @e[type=minecraft:ender_dragon] and the end gateway appeared.
[Edit 2] I gave myself 4 more crystals and beat the dragon manually, but no obsidian block by the perch. A third gateway now appears.

This happens to me as well! I updated my world from 1.19.3 to 1.19.4 and no new gateways can spawn too!

This is happening in my single player world for both 23w13a and again today in 23w14a.

Background: I started my realm in 1.19.3 and killed the dragon before the update. After we updated to 1.19.4, we respawned the ender dragon and it did not create any new gateways. I fixed this issue by downloading NBTExplorer, navigating to [MyWorld]/level.dat/Data/DragonFight and then changing "NeedsStateScanning" from 0 to 1. I then had to kill two dragons. The first one did not spawn a new gateway, the second one did, and in testing in a creative world, any more dragons killed after the second also spawned a new gateway. It seems changing the NeedsStateScanning tag resets the counter on ender dragon fights, so the first one killed attempted to respawn the existing gateway (from our original fight), and the next 19 would spawn the next (non-existing) 19 gateways.

I can confirm that Brian81505 method below is accurate to reproduce. my world which is now (unfortunately) 1.19.4 with 14 Gateways will no longer generate any more. Reverting a 1.19.4 world back to 1.19.3 does not fix this problem
However 1.19.4 generated worlds also will only create Gateways up to when you log out. As soon as you log out it stops generating.
My theory is that this is a problem with loading a 1.19.4 world. When killing the next dragon it doesn't remove an entry for the "World" > level.data > DragonFight > Gateways * entries
Since it doesn't go down in numerical value it's not correctly identifying the dragon is killed and it needs to spawn a gateway at the next location at the bottom of the list.
Do not use 1.19.4 if you want to spawn all gateways.

I tested this in creative.
I killed the enderdragon twice in a row and spawned both gateways.
I then left the game and rejoined.
Then I killed the enderdragon another time and no portal spawned.
I then killed the dragon again and still no portal, but the 3rd time a new portal spawned.
I did this up to 5 portals, then left the game and rejoined again.
I then had to kill the dragon another 5 times, and on the 6th time a new portal spawned.
It would seem like the data for the amount of times the dragon has been killed hasn't been saved as has been said by a few other people here.
This would also mean if the dragon is killed 19 times in a row without leaving and 19 gateways have been spawned and then you happen to leave the game, you'd have to kill the dragon an additional 20 times before you can spawn the final end gateway.
Looks like I won't be making my end hub anytime soon :,)
(This was in 1.19.4 in singleplayer but this issue has also affected my server on the same version)

Think I can help confirm that new gateways are spawning on top of the old ones, I had a flat platform around the original gateway (from the first dragon), after killing a second and third dragon the adjacent blocks around the gateway are missing (not broken by the dragon) and no others have spawned. World wasn't created in 1.19.4 but it's on that version now.
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About the last comment : I play a world on hardcore and started it in 1.16. I killed the ED in this version, and about 300 minecraft days later I updated the world to 1.19.4
Again 100 days later I re summoned and killed the ED 19 times in a row (in 1.19.4) without even looking at the portals.
After that is counted them : 11 portals. I just wanted to kill myself. I found this page and checked my first gateway : 4 cobble blocks near this portal have been destroyed, but not the trapdoor to access it. It confirm that the game dont delete portals but instead place them on the old one .I really hope it will be fixe soon because I cant destroy pillars until I have 20 gateways and I can't continue my end project,
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I have this same issue, friend and I killed dragon and first portal spawned. We killed it a second time and 3rd and no end city portal. No idea why.

My issue got taken down saying it’s a duplicate of this one. I specifically said I didn’t leave the game after the dragon was spawned before killing it. So why did mine get added to this one ?

As long as the world is left between dragon kills, this is the issue; whether the dragon exists while leaving is not relevqnt to this issue.

1.20 Pre-release 1 bug still exists however there is a new bug that does not happen in 1.19.4
If you spawn the dragon and then quit the game, when you rejoin and kill the dragon the entity is removed but the health bar, fog-of-war are still there. You cannot summon or /kill as 'entity does not exist' and the end portal hasnt spawned allowing you to summon a new one
@unknown, the other bug you're talking about is tracked separately in MC-262557.

Same issue still happening in 1.20 pre-release 4

I used to play my hardcore world in 1.19.3 and beat the dragon 7 times, I have 7 gateways. Then I moved to 1.19.4 and tried to beat it again. I want to get all 20 of those and after I killed 3 of them I see that there are just 7 gateways.
It seems that how many dragons I kill the first gateway gets replaced. I tried it in a creative world.
Getting back on 1.19.3 and trying this in the same world doesn't solve anything. I even tried to modify some things with NBT Explorer in the level.dat , Dragon Fights. I changed some values, played with the settings but nothing is working. In Gateways entries is says 20, but there aren't that many.

If you were on one of the versions with the problem, it's like the "dragons killed counter" was always reseted after each logout. So after updating the world to the latest release after the issue was resolved, only the counter calculation formula is fixed, but you are still at "zero" ragardless of how many dragons you killed.
I had only one gateway in pre-release 5. Then I updated the world to 1.20 pre-release 6 (when the issue was fixed).
Then after killing the dragon again, my first portal was recreated (the blocks near it were excluded) and no new end gateway was generated.
The second kill onwards worked perfectly as intended. I could logout and each dragon kill was still generating a new gateway.

Can confirm fixed with 1.20-pre6 generated worlds
If you update your world to 1.20-pre6 (or release version when ever that happens) You will need to kill the dragon atleast 20 times again. I had 15 portals active, updated, on tries 8,12, 15,17, and 20 my last 5 portals were spawned in.
*I did this in a back up of my world and then just copied the 1.20-pre6 DIM1 file to the 1.19.4 save file and its worked fine. so atleast i now can start my end project.
Thanks [Mojang] Panda, you're the best
Please provide me the world that you defeated that dragon, for now I cannot confirm this behaviour.