when player is under the water and swim upwards if there is a block above it will get inside the block, if you try to move either back/forward/left/right and there is another block will phase and it will start getting damage. the only way to avoid this is going down from the first block. 

same thing happens when you have a water source running, for example on a tunnel, if I try to jump to get out, even if it is 2 blocks high the player gets stuck for a second and receives damage, if I move to the left or right and there is another block I will get stuck and will receive damage.

also when it rains and you walk under 2 block high it will get stuck.

after sleeping helps or restarting the game stops this behavior, but I'm not sure what starts this behavior.

No this Do not happen with elytra, only when player is in contact with water even from rain.

this is way different from MCPE-109925

try go mine into a cave make a 2 block high tunnel put water and try to jump you will get stuck, that is the easy way to replicate this. No Elytra involved .