It's kind of hard to explain so here's a video of it happening, this only happens when the chunk is not loaded (ex. leaving server and opening a single player world for about 4 minutes, then rejoining server) or sometimes when the server reboots or simply just rejoining a server.

Steps to reproduce: 

1. Place down a boat in one chunk, and then on top of it place down another one in a different chunk (see image below)
2. Reload the world/chunk/restart the server

Expected result: The top boat should stay on top of the hitbox of the bottom boat. as shown in the photo and first part of the video.

Observed result: The top boat slides off of the bottom boat.

This farm is based on this design by Rays works: https://www.youtube.com/watch?v=sT4noYO1xUE&