The question is, did the company charge for, and did you get paid for the additional time it took to complete the job? I've been in similar situations, but rarely ever got paid for the additional time it took to make the repairs.
The worst incident was in the mid 1980's when working for an Oldsmobile dealership. A "customer had one of the infamous Olds 5.7-liter diesels go bad. He took it to an independent garage to have it repaired. Once the engine was out of the car and disassembled, he decided it was too expensive to have rebuilt. He brought it to the dealership to get some "warranty assistance".
I was the one unlucky enough to get the job. The vehicle came in behind a tow truck with the block in the back of the truck, and 22 boxes of parts in the interior and trunk of the car. At the time GM paid a little under 30 hours to R&R and rebuild the engine. However, since they were such problems, they decided to arbitrarily cut the time. Between the time I started on the rebuild and the time it went out the door they cut the flat rate almost in half. Then they decided since the engine was already disassembled, they would only pay a little over half the flat rate or 9 hrs. Of course, they didn't tell me that until the job was done, and the car was out the door.
Needless to say, the reduced pay didn't set very well with me. I knew I couldn't make ends meet if every time someone complained I didn't get paid for 20 hours of work. That's when i decided it was time to move on to a new career.