When a player is in a boat, often they go invisable also once the boat is broken, the player usually is invisable for around 1-2 mins. Same goes for minecarts, it does this with all mobs and players.

Reproduce:
Get player A to get into a boat and boat around for around 1-2 mins.
Player B watch as the player goes invisable.
Player B Break the boat after around 5 mins.
Player A will now be invisable.

It may be possible this only happens IF you do not see said player actually mounting into the boat.