Q: Should I have concerns on a check engine light flashing for 2 seconds just after startup and acceleration?

Last month I ran out of gas and AAA gave me 2 gallons of gas. Since then, the pump would click off when filling up and the attendant would have to manually pump the gas to the tank. I also experienced slight performance issues, where the engine seemed to lag under 35 mph and getting poor mileage. The dealer determined a couple of caps the size of half dollars were stopping up the filler tube.

Issue resolved, filling up is fine now. The cars runs ok, but I don’t see any marked improvement in my gas mileage. Then just this morning, after backing up out of my garage and accelerating down the driveway, the CEL flashed on for literally just 2 seconds, then off. It was during this time I felt a slight buck and thought it might stall in the driveway. But it was fine going forward. My concern is that the car never did this prior to when I ran out of gas and still doesn't run 100% like it used to. Dealer says not to worry, but my intuition says something is still wrong. Thoughts?

My car has 13500 miles.
My car has an automatic transmission.