rights to sue for cost of repairing home improvements

Today I was in Special Civil Court in New Jersey because I was sued for monies owed to a subcontractor. I was sued in the amount of $25,000.00. all transactions were made in cash and the subcontractor had poor records. The issue of poor workmanship was mentioned but not pursued as part of the case. I tried to prove the best I could that the bills were paid in full according to records available. The subcontractor won $2,800.00 based on what the judge felt he was still owed for his work. Since I did not counter-sue for poor workmanship and repairs that need to be done can I file a new complaint not a countersuit against him for the cost I will incur to fix mistakes. While we were in court the only thing said was that both sides agreed not to make the mistakes/repairs an issue in the present matter. Now that this is settled can I file my own suit in small claims court?

Unless the issue of poor workmanship was adjudicated in your recent action, you should not be precluded from a further filing on an unresolved matter.

However, you need to be aware of the appearance of a retaliation suit.