Apple skin is mostly insoluble fiber, which means it's harder to process. That's likely where your problems are coming in. To be sure, try eating the peanut butter with something else and/or the apple without the peel.
I don't have problems with peanut butter in moderate amounts. But if I get on a kick- eat it two or three times a day for a couple of days- I do. Of course, that seems to be true with just about any food I crave.