I have found several bugs in the BTS Ontime database, all the fault of the airlines themselves. I have reported them to BTS (and they were very helpful!), but I will document them here, as some of them are not completely fixed:

Southwest Airlines reports all of its tail numbers incorrectly. They truncate the letters from the end of the tail number, reporting, e.g. N524 (which does not exist) when they mean N524SW, or N446 (an amateur-built aircraft) when they mean N446WN (their Boeing 737). As of March, 2004, Southwest has fixed approximately 30% of their aircraft.

US Airways severely over-reported one plane, N183UW. It seems that they reported three separate planes using the same tail number somehow. As of February, 2004, this problem is completely solved. Thanks, US Airways!

American Eagle reports all of its tail numbers incorrectly. They append 'MQ' (their carrier code) onto the tail number in the place of 'AE', which (as far as I can tell) is actually on all of their tail numbers. For example, they report N514MQ (which does not exist) instead of N514AE. Worse, some of the tail numbers they report are actual planes registered to other people, for example, they report N840MQ (a 1982 Cessna 550) instead of N840AE (their 2002 Embraer EMB-135). As of July, 2004, this problem is completely solved. Thanks, American Eagle!