Your bag was not loaded at BOS for reasons other than the boarding pass used. It does not matter which boarding pass you use. There is nothing you can do to prevent this from happening again. The tag will always be an AA issued one if you check the bags with AA, but the flight number on the tag will always be the prime flight # of the operating carrier (BA in this case). You did not do anything wrong. Thousands of people do this every day and their bags arrive. You were unlucky that yours did not.