If the Company paid into a pension for the benefit of general employees or directors that is a company expense, nothing to do with director's pay. There is a factor based on age of director which is multiplied by the director's remuneration to find the limit of what the company can contribute.
If the pension is a personal one, and the company paid on your behalf, yes it is a benefit in kind, but cancelled out by the amount you can claim tax relief for.
Assuming you did not contribute more than allowed percentage of your relevant income ( goes on age) I would agree you have overpaid Prsi, and should ask Revenue to send you out a form to do an amended P35. It's not an unusual request; they will take a few weeks to process the refund though.