As mentioned in another post - the damaged vehicles will no longer be deployable whatsoever, in the forthcoming EXE.
For now - don't use the "deploy all" or "auto deploy" on a human campaign core. Nor should you pick things directly off the formation list when deploying your forces.
If you have damaged units carried over in your core - the damage points on the cripples are credited to your opponent at end game as VP, as is normal. Thus being forced to "carry" damaged core helps your opponent.
Moral - protect your core troops!
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If damaged already, and they become destroyed (easier done with badly damaged cripples) then even more damage (VP) will be credited to your opponent.
Plus they are in danger of having the crew destroyed thus losing some experience in those units.
Leave any such on the grey hexes at the rear of your deployment zone is best, should you have made the mistake of deploying them. They will then be removed from the map, like any other retreater/router.
As said - that problem is fixed in the new EXE.
Cheers
Andy