After some tests it seems that the original problem for which I opened this case is part of a more generic problem.
The problem is that a unit (player/AI soldier) can get negative score when destroying apparently enemy vehicles (a vehicle can be a car, tank or ammobox).
For instance if I am a soldier on BLUFOR side and I shoot and destroy an apparently east ammobox ("Box_East_Grenades_F") I get negative points (which is not what most players would expect). Why negative score points? I figured out it must be the vehicle's class attribute called "faction" (aka side) that is used by the score system to give negative/positive points to the unit that destroyed the vehicle. For instance the "faction" attribute of "Box_East_Grenades_F" vehicle has a value of "Default" which must be the civilian side. When a unit destroys any civilian sided vehicle it gets negative score points.
This is problematic in a mission I made because some of the respawn points are ammoboxes and if a unit destroys the enemy created ammobox (to prevent the enemy from respawning near) it gets negative score.
Suggestion: let the mission maker decide (through editor GUI interface and scripting command) to modify the side (by modifying the value of "faction" attribute or additional attribute used as a modifier for the score system) of the vehicle (this will solve the ammobox problem). In addition to this the score system should use the value returned by the "side" command when applied to the vehicle (this will solve the initial case problem when enemy gets inside friendly vehicle).