At 90+% apparent attenuation, I would also be suspecting something wrong, as you are. That being said, I would check the calibration of my hydrometer and thermometer. It could be that you were actually mashing several degrees lower than you thought and getting an added boost in fermentability. I also had a brew several years ago that finished at 1.003, well below the target of 1.014. Subsequently, I discovered that the tab of glue which had held the scale in place inside the hydrometer had separated and the hydrometer was well out of calibration (and subsequently worthless since the scale would move up and down with a gentle shaking motion).
You said that your carboy is scratched, is this a guess since you think you have an infection? I've found that a small amount of diluted solution of iodine shows up scratches very nicely in plastic pails, not sure if it would do the same in a carboy.
Since you already have this bottled, I would let it carb up and check it again once it has reached full carbonation. If you can't taste anything odd, take a bottle to someone you trust who has good smell and taste senses (a BJCP judge would be a good choice) and see if they can detect anything.