It's a common joke that nobody understands the grapple rules, but in reality it's only two or three pages of the PHB. What is it about these rules that has caused so much confusion and annoyance?
Almost-certainly not a comprehensive list, but some issues that come to mind for me immediately:
They are rarely used. Grappling is a fairly ineffective tactic, requiring specialized feats and at best only causing problems for a single target—and there are a lot of ways to get out of it.
The process is very particular. There is a very specific sequence of steps, each with their own ramifications and limitations, which means it’s a very dense “two to three pages.”
“Two-to-three pages” is a lot to look up in the middle of combat when it suddenly comes up. You might not memorize all of the details of a given spell, either, but spell descriptions are usually a paragraph or two.
Grappling is very unlike all other forms of interaction in 3.5e. That makes it very difficult to keep track of, because human brains remember things by association and pattern. All we have for grappling is that it’s different.
Being different also robs us of any confidence or sense that we “get the gist.” It doesn’t match up with our intuition of how things proceed in 3.5e. It may not be counter-intuitive, per se, but it isn’t intuitive, either.
But if we’re being honest, there are things in there that are counter-intuitive. The interactions and conditions applied to each side at different steps in the process have a lot of implications and some of them are not at all what you would expect.
For what it’s worth, I’m still apologizing to the last DM I made look up the grapple rules. We laugh about it, but it prompted some pretty absurd situations, and also took a ton of time to figure out in the middle of a session. It was not good for the game, no matter how much it was the “right choice” for my character at the time.
KRyan has a lot of good points directly from 3.5e, but Grappling, in general, is fraught with difficulties, and D&D has had its share. In AD&D, grappling was based on ability scores and size, which meant even the mightiest warrior feared being grabbed by a group of Ogres. AD&D 2E had percentile-dice grappling that determined what would happen.