Some of the underwater plants that are 2 blocks high sometimes generate with the top block out of the water. That top block still has the swaying animation as if it was underwater, even though it's not. Probably these plants should either only generate when the entire plant can be underwater, or the top block should not animate when it is in air.

This is working as intended. If the bottom of the plant is moving why wouldn't the top be?

Ah I didn't really sorry. The animation read to me as if the plants are suspended and "floating" in water.