Actually I had a similar experience some years ago, on a TWA DC-9. I happened to be sitting where I could see both ailerons. We were in the last stages of taxi. One aileron was full up, the other full down. This did not look at all right to me. I flagged down the attendant as she made her way to the back crew seat and pointed this out. She fairly sprinted to the cabin and sure enough, we pulled out of line near the threshold. I saw the control surfaces move and the flaps deploy and stow a couple of times. A crew member came into the passenger cabin and took a quick look. The captain apologized for the delay and put it down to instrumentation problems. After 10 minutes or so we were underway. No harm in using the meatware this way
Ailerons on DC 9 and MD 80 are aerodynamically controlled by tabs, so the ailerons may stay in any position during ground ops. Same with the elevators. What you saw was perfectly normal.