I had a similar experience on Friday flying SFO-SEA. I was originally on AS223, but late the evening before I SDC'ed to an earlier flight, AS331. At that time I checked in and was issued a mobile boarding pass. The next morning, I notice the mobile app says I'm still on my original flight (223), upgraded to first class. Which is odd, because I still have a mobile boarding pass for 331. Customer service couldn't figure out what had happened (confirmed I was still booked on 223, but also showing up on the upgrade request list for 331). They were able to fix it, and I assumed it was just a conflict with the upgrade process upgrading me on my original flight soon after I had switched to the earlier flight.

But given the OP's experience, maybe there were other issues going on with SFO-SEA flights this week.