I've recently noticed 2 bugs with villagers on EMC The first bug require a 1*2 hole with 1 villager in it You just have to trade with him while holding a villager egg to get a tiny villager beneath him. For example, I saw a toy villager at FatAndy's res. Secondly a disappearing villager bug, The villager have to be surround by 4 blocks and with a block above him and only 1 block under him( so if you destroy the block under him he will fall. After a while the villager will fall all the way to the ground!?
This is desired behaviour. Minecraft added it in 1.4. As for the other thing, can you record a video of the problem?