I see this happen usually around mountains in strategic... it's like the height values of the terrain is messing with the cursor. What I've done recently is switched my view point to 3 (I think - it's the one where you look down and tiles is aligned like boxes instead of diamonds). I haven't encountered this problem with it in this view, maybe give it a shot?
As for tactical, I don't seem to have this problem unless you're talking about the battle with Abeix... that is just another beast all together.
Was talking about trying to use the bite attack off my 2 ophidians I had trained to level 3 and 4... Sadly they died cause they decided to disobey >)
But as said before, it is infuriatingly hard for me to try and use stun attacks, and bite attacks in melee...
The mountain stuff, well I wish it would be fixed, but atleast I made my game auto-save each turn, so if it messes up my game terribly I simply reload (Like troops deciding to move away from my city, instead of into my city, when enemies are at the gates. (I like to build my cities next to mountains and hills, even though the map is going to look like crap afterwards).
Sincerely
~ Kongdej