There is more than this issue.  Anything that happens simultaneously seems to 'lag' updates, even the spells themselves.  Or even like in the case you mention, circumvent it.  I when clicking on units while 'stuff' is going on, or some spells or attacks that have multiple targets / hits will cause animations not to update.  Prone creatures stand, health displayed is incorrect...I've even gotten units to stand in a place that they were (oh dear) but aren't actually anymore.  I think it may have something to do with multiple core use (wild guess). 

I think mousing over is related since it calls for the health instantly, while the artsy side of the program is waiting for the animations to finish before updating the effect of the attack...even though the game already knows the result.

I think a bunch more testing with mad clicking around and massive spellcasting / healing / blowing units around needs to be done to find out what causes the hiccups.