Ok,I sort if had this problem a while ago when I tried Helicopters in TO.
I was pretty sure it was becuase I messed around with the section
thats like;

[Cliffs]
Hover=100%

However,I tried again this time leaving that section well alone.
When I put in my first in the game helicopter it seemed "ok",on a few occasions it halted and didn't want to move,but it was nothing horribly serious.Then when I put the 2nd helicopter in, disasters struck.Its as if certain areas of the map are damaged or something,the helicopters get jammed in places,no where obvious like a bridge,but normal terrain,other units get stuck or can't enter certain cells/areas,also this affects buildings,some  buildings will have red squares not allowing me to build in them in perfectly normal zones.



The only thing I changed was the hover height but I really don't see how
it should mess things up like this.

btw that jet is landed and not airborne