If player's head is slightly above water no breath bar will be displayed in the bottom bar, but the player will start to suffocate after a while.

I believe what's going wrong is that the player is rather A: slightly above the water causing the game to get confused and then decides to make you suffocate as if you were really underwater, or B: The player's head is slightly BELOW the water, but breath indicator doesn't display.

NOTE: The breath indicator will show at the right time, but in this case the position confused the game.