If you don't toss the bobber away from your at least 5 blocks away from you when it reaches the top of the water, it'll rise out of the water but still act like it's moving when it's in the water and you can't catch anything that way. The attachment below shows you what I'm encountering. I'm one who likes to fish on this game.
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This issue is a duplicate of MC-11877. It has been linked to the original bugreport.
Please search before reporting any bugs, as it's likely that one exists already.