I know from previous Battletech universe video games, and my vague memory of the table top game, vehicles are not supposed to survive being stomped by mechs, much less DFA by mechs. In missions where vehicle kills are the goal, I often run into vehicles that take 3+ stomps to destroy, and which kill mechs that DFA them, while the vehicle remains in service after the DFA. Is this a bug, or is this by design? If by design, is this a departure from table top rules?

Depends.
Are they Unimogs? If so, everything is working as intended. Nothing short of a nuclear explosion will stop an Unimog.