Not really a glitch. The enemies may not be very smart, but they aren't going to dive down to you and risk killing themselves. Maybe in the future, there will be swimming enemies.
I don't see how skeletons and zombies could drown anyway. And when I think about it, I'm not sure how they'd swim, either. By my logic, they should walk along the bottom completely unaware that they're even underwater. The only time they should try to come up is when you're above them.
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"Look! Grass underground! It's thar!"
"Don't be a smartass."
"More like smartgrass am I right?"