Interestingly enough, on my last trip, finally, I was able to check in on the iOS app without having auto-check in automatically go. I did the same thing as I always do - check in like normal, and before selecting my mobile BP, I unchecked the auto-chekin for return journey (or whatever it says) box. Usually, it auto-checks me in, anyway. This time it didn't.
As for the seats changing, I've never had that happen to me.