under some circumstances, mobs will stop bobbing in water. the attached picture illustrates an easy way to reproduce the issue.
put some sheep in the cell
dispense the water. the sheep bob in the flowing water
break the yellow glass and let water spill out
replace the yellow glass. the sheep no longer bob in water.
Just experienced the same bug, cannot get the entity to start bobbing again no matter what I try. Once I kill the old entity and spawn in a new one, the new one starts to bob.