Satellites and WPs seem to be destroyed one at a time, just like you'd expect. The first one in the stack soaks up all the hits until destroyed, the number of the stack is decremented by one, and the battle rages on.
With fighters, OTOH, it seems like the whole stack is wiped out when the first fighter goes.
Actually it seems to me if the sattelites and WP's have shields the damage is done normally. With no shields all in the stack seem to die when the first is destroyed. Try putting small shields on the fighters till the bug is fixed. I haven't seen the AI use shields on fighters so I don't know for sure it will work.