These are just from what I've discovered and will be updated over time. Keep in mind I might be wrong about these but I wouldn't list them if I wasn't exceptionally suspicious. I also totally get that the majority of these are non game breaking and don't require immediate fixing; I just figure it would be useful after the big things are out of the way.
1) Animals run full speed in shallow water and can run over deep water.
2) Drinking from a boat doesn't play the drinking sound file.
3) Sometimes when building fences, after you place the initial corner post and extend once flawlessly, you can't extend anymore without surveying (even if the land is perfectly flat)