Yes, I tried searching the web for this problem, and all I got were links to default eye replacements, not issues with them. The eyes (which I was looking for non-defaults, but I accidentally downloaded the default version) actually broke EA's eyes. Their eyes are literally just circles of color. There are no pupils. These are the eyes that caused this. It wasn't a problem at first, but then when I made a supernatural sim, the eye glow didn't correspond with the eyes and that irritated me, so I took the mod out and then when I went back into the game the eyes looked like that (And I did try to make a brand new sim, and the eyes were the same way). If anyone has had that problem, please let me know how to fix it!
Here is a screenshot

Pretty sure that EA eyes aren't broken if you placed the *.package wihtin your Mods\Packages folder in your Sims 3 userdirectory (Documents\EA\Sims 3). They might be still in your Cache Files, try clearing those out (everything that's CAS Cache related) and start game, reload save.

Then see if their eyes are reverted back to EA's defaults.

There are multiple cache folders, which one is the one I need to clear? Or all of them? This has never happened to me so I'm slightly confused.

Those within the Sims 3 user directory and those in the Thumbnail Folder. If you're playing a custom world/EA Store world, also the ones in your WorldCache folder (UNLESS you're on a Mac!!). That should usually clear up all the messes.

Um, ok, I just tried doing that and it didn't work!

Okay, I found out that it wasn't that mod that did it. It was a different one. It was called ContactBaseEyeReplacement.package. I have no idea where it came from, but it wasn't a glitch, it was a another mod that I don't remember getting.