If you are talking about the current time, you would say "The car has broken down."
If you are talking about the event in relation to some other past event, then you would say "was".
"When we looked at the car, we found it was broken down."
Note that in this case, you are saying the car was in that state, but you don't know when it broke down.
If you are talking about a situation where the car broke down after an event, but was working before the event, you would use 'had'.
"When we got back from the trip, we found the car had broken down."