Putting skeletons and zombies in some water will just drown them. They will make no attempt to swim up unless you hit them.
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If you dig 3 blocks down, put a water source at the top, and then spawn a skeleton at the bottom it will not swim up. However if you place a skeleton in the source block it will swim. I have a couple screen shots if you need it but I don't think it's necessary.
Tested positive it appears that mobs may not have enough strength to fight the current.
I did some more testing and it seems it has been in since at least 1.2.5. This may not be a bug but in my opinion mobs should still be able to swim up.
I could get it working if you fill all 3 blocks with sources.
Yeah but not if its flowing water.
Confirmed.
Steps the repeat:
make a 2x2x3 deep hole fill only the top with water. spawn mobs on the bottom. They will stay there till punched.
Edit: You can also punch them back down to the bottom and they'll get stuck again.

Mobs can only swim upwards in source blocks, not flowing water. Otherwise, they could swim up waterfalls. Then again, the player can...
This behavior is extremely useful for mob drowning traps. Whether that's a strike for it or against it in the developers' eyes, I don't know, but this behavior has existed for a very long time without being changed.
Yeah I realize that now. How do I delete this bug.
Could not confirm. Please give more detail in your reports.