The boat "lid" isn't working quite right. It sometimes still lets water render in the boats, as it appears to flicker in and out frequently; and other times it renders part of the player/animals invisible, since the lid renders before the entity inside the boat.
To Reproduce, just enter a boat (if the boat is filled with water, exit and re-enter it).
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Can confirm.

@anyone having this issue: Please force a crash by pressing F3 + C for 10 seconds while in-game and attach the crash report ([minecraft/crash-reports/crash-<DATE>-client.txt|http://hopper.minecraft.net/help/finding-minecraft-data-folder]
) to this ticket.

Crash file produced while looking at boats with flickering water texture inside.

Results of the short survey to see if that effect is graphic card / driver dependant:
1 Intel:
OpenGL: Intel(R) HD Graphics 4000 GL version 4.0.0 - Build 10.18.10.4276, Intel
3 NVIDIA:
OpenGL: GeForce GTX 980/PCIe/SSE2 GL version 4.5.0 NVIDIA 358.91, NVIDIA Corporation
OpenGL: GeForce GTX 750 Ti/PCIe/SSE2 GL version 4.5.0 NVIDIA 358.91, NVIDIA Corporation
OpenGL: GeForce GTX 970/PCIe/SSE2 GL version 4.5.0 NVIDIA 353.30, NVIDIA Corporation
@@unknown: Your drivers are outdated: Update from http://nvidia.com/ this is unrelated to this issue

Confirmed for 15w47a

Confirmed for 15w51a-b

See the Screenshot in the picture on this Ticket of the Enderman – MC-92870
This might be a better lid for keeping the water out as it would cause no issues for Mobs, but would delete water.

Confirmed in 16w02a.
Water renders flickering, and is inside the boat.

Confirmed for 16w03a (Even though it was already stated), however it changed a bit;
I don't see any water flickering inside the boat in 16w03a, however the entities' lower part still unrenders.
This issue has been fixed in 16w04a

Boats don't render entities beyond the point at which they enter the cavity of the boat... This can been seen in the case of banners placed in one-high water: boats sliding into the banner clip out the portion in the boat. It seems to be related to this.
Occurs in Minecraft 1.10.2 . Is this a separate issue?

Yes.