Shifting problems after removing and replacing rear wheel I had a mysterious flat tire on my rear wheel after I had left the bike standing for the workday. I removed the wheel and changed the inner tube. I didn't think anything went wrong while doing that (e.g. I don't think I bumped the derailleur) but I did notice that the brake disc was rubbing slightly on the inner pad, so I adjusted the pad a tiny bit and it seemed to be fine. The disc wasn't visibly wobbling when I looked at it between the brake pads.

On the ride home, the chain was sometimes skipping on the rear sprockets and I had frequent trouble shifting. I suspect that the derailleur is misadjusted. Both the chain and rear cassette are pretty new, and I had no skipping problems before I changed the inner tube.

Before I try adjusting the derailleur, is there something else I should check? Is it possible that the quick-release skewer is too tight or loose causing the wheel to be misaligned?
Per your comments, looks like you just needed to re-seat the rear wheel.  To be fair, I will say there are things you can do while changing a tire that may cause problems like this.  But having to adjust the disc brake, then the shifting acting wrong is a dead giveaway that the wheel went back in a bit of a different angle than it came out.