Yes. There was a problem with the framing on both Part 2 and Part 3. The Part 2 problem was very noticeable--I never did figure out where the Part 3 problem was.
If you want to check, the easiest thing to do is pop in the Part 2 disc and go to the part where Marty puts on the jacket that automatically sizes itself--you can't see his hands which show the sleeves sizing themselves. Also, a little later when he's on the hoverboard in the middle of the pond in front of the city hall, the frame is cut.
All in all, I believe it was about 5 minutes worth in Part 2 and 2 minutes or so in Part 3.
Starting at the end of March, Universal started releasing all their sets with the new discs, but if you bought the set before then, the discs probably have the problem. From what I understand, if you look at the back of the box in the spec grid, there should be something that says "V2" or something like that, signifying the new discs. If not, you have the old ones.
If you have the old ones and want to get the replacement discs for free, just call 888-703-0010. I don't know if the number is still working--I assume it is--but they'll ask you your address, then send you an envelope that you put both discs in, and they send them back to you. It's pretty simple, but might take some time. I did it a couple months ago.