I seem to remember that on my first playthrough, I found Gizamaluke an absolute pain in the backside. Is that the bit you might have got stuck on? If so, I definitely sympathise.

The only other bit I recall that gave me much trouble was Ark. I replayed FFIX in November and I have to say I didn't find anything terribly difficult. This was my third/fourth time through, and I have to say there was only really Ark when I expected any real bother.