This is how I read it:
"I wish my car never broke down" This is referring to an on-going state of your car. For example, one might say:
"I wish my car never broke down, but it does all the time." I think these are both present tense.
To refer to a specific event in the past (of the car breaking down), you would say:
"I wish my car had never broken down."
OR
"I wish my car had not broken down."
OR
"I wished (past tense) my car had never broken down"