To answer the question in your title "How Common?"...its not very common at all. In the past 2 years of flying ~125K miles, it didn't happen at all to me.
Well, AA flew 282
billion seat miles last year on about 2.4 million flights, so your 125k annual miles aren't even a drop in a bucket...
One potential reason is there were some seat duplications perhaps due to an IT issue (perhaps related to an equipment swap) that they thought would be easier to sort out by getting everyone off and re-boarding.