Easiest way would be for weapon switching to trigger reaction fire after the action is taken. Or, better yet, take the scores both before and after the weapon switch and take the lowest of those two values and use that for judging reaction fire. So if you're switching from a rocket launcher to a pistol, you won't be lightning quick in putting the rocket launcher away.
Can't really suggest the easiest way to approach that without knowing all the intricacies of how the whole setup is designed.
That said, I've noticed two bugs, once of which has been mentioned:
Light scouts often don't have a sprite; there's just a door and a black blob, but once I open the door the inside looks normal. I initially thought that it may have been due to the craft's footprint not being entirely on the map, but I'd need to see the bug again and compare it to how it should properly look.
The second was on an arctic map, when my troops were deposited sans dropship. That is to say, all eight of'em were unceremoniously dropped on the corner of the map...which just so happened to be right next to the downed scout. Not quite sure how that happened, but I never saw it in my prior games (Then again, arctic maps aren't exactly common).