Here's a few examples... I'm just scrolling through the list quickly through zyrthofar's editor:
1) Waterbug - It is weak vs lightning, but fixing "magic evasion" will require you to have Cecil inflict damage on it prior for Thunder to be used... or it would very likely survive the attack.
2) Alligator - It is weak vs ice, and you get a nice free Ice Rod in the dungeon you find the monster in... but the item magic would simply fail to work due to its low spell multiplier (it's 2, where the Alligator has a magic evasion multiplier of 3).
3) Ogre - Stealing MP from an Ogre is a pain in the ass. It has a magic evasion multiplier of 3... and Tellah's "optimal" Wisdom/Intelligence stat is usually @ 24 (spell multiplier of 9) and that would actually slow down his MP absorption...
I'm sure I could find more examples... but the point is that the game's stats aren't perfectly balanced for the "buggy" code.

4) Tinytoad - Edge's Flood would be ineffective, due to his low INT stat. The monster has naturally "high magic evasion", which limits Rydia to do magic damage.
5) Plague - The match would be a lot more interesting when it does have quite a bit of magic evasion to play with...
6) Most monsters that you could fight in the "Peninsula of Power" north of Mt. Ordeals would murder you... Palom would not have enough INT to damage them through their magic evasion... everything would rely on DK Cecil's Deathbringer.
7) Mechanical Dragon - That monster suddenly becomes an even bigger pain in the ass.
8) Fiend - Casting Mute on them is a pain in the ass... the MageMasher is the solution, but that might take a while...
9) Most moon creatures would be tougher to kill with Leviathan, given their high natural innate magic evasion and Rydia's INT isn't probably where it should be.... (especially with suboptimal equipment).
10) Octomammoth would make Tellah obsolete. Rydia would struggle to produce damage vs it with Chocobo.
11) Cagnazzo finished off with Tellah's Thundaga early in the match? Think again!
12) Rubicante wouldn't really be harmed by Rydia... unless it's just Chocobo while his cape is open... Edge's Ninjutsu is a wasted effort.
13) Odin's match would be that much harder...
14) Leviathan would survive a few Thundaras for sure.
15) EvilWall would be a nastier beast...
There we go.