I've had villagers stuck in various places in all three VV games. Some dangling helplessly from top of a hut or stuck at the side of a hut. It's actually quite funny watching them turning back and fourth while their little feet are feverishly running nowhere.

I had a very helpful glitch in VV3. I needed a break after completing some of the first puzzles. When I returned to the game, the puzzles, I had resolved, was in scrambles; lift, alchemy lab, beehive, etc. After fixing it all it was time to get back to harvesting honey. Suddenly I see my poor farmer run for her life, with the bees in full pursuit. After LAMO, I investigated and sure enough the beehive, which was nearly empty, was now loaded to its full capacity.