Well, lots of reasons.
Some ROMs simply get renamed. These are easilly fixed.
Some ROM sets have additional or repaired ROMs added. This is usually because the first dump was missing a rom, or got a bad dump that wasn't discovered until later.
Some ROM sets get a new "version" added in. Usually not much of a problem. Just download the new child set and everything works.
Sometimes, the "parent" version chages. NOW we're talking major hair pulling. The previous "parent" rom is now a child/clone and some new ROM is set up to be the "parent" because it's newer. Lots of files change places, since the "parent" is set up to be the only "complete" game in the ROM set, and the children/clones should only have the "different" files.
And finally, some ROMs are just simply completely brand new.
That's why it's a major pain in the butt to maintain a ROM set.