I loathe auto check-in and really wish CO would do away with it. Errr, I mean the new UA. This is a pmCO feature that they kept during the OLCI process.
It's bitten me twice in the last month alone. First time using the Mobile App after I did check-in I saw that the auto upgrade feature was turned on. I turned it off but apparently it didn't "stick". Second time was last week. After doing OLCI on a normal web browser on a computer it auto checked me in for the return. I was shocked to see the boarding passes for my return flights show up in my inbox 24 hours before departure as I always uncheck the auto check in feature during OLCI.
-RM