Because of the fact that score is computed based on object config attribute "faction", destroying a friendly vehicle that was captured by enemy will add a negative score instead of a positive one.
Suggestion: change the score computation mechanism to be based on the effective vehicle side (determined by the side of the unit controlling the vehicle).
A script command with global effect should also be made available to set the effective side of an empty vehicle. This can be useful in missions where the objective is to destroy an empty object like an ammobox. With the current system destroying an ammobox will add negative score to any player (because the "faction" attribute in the config for the ammobox is set to Default/Civilian).