I am currently modeling a character. The face has a mirror modifier on it (not applied yet), and the eyes have been mirrored (applied) and separated, with a lattice acting on each. The lattices have basically been mirrored, (I used Scale X -1), so I know they are the same. However, I noticed the eye sockets don't appear to match up horizontally. If you look at the picture, I have created a small green box that is mirrored, and you can see the difference in the eye socket. I also added the red lines for more reference points.
If you follow the red lines and the green box from left to right, you will notice that the right eye socket appears to be shifted down.
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$\begingroup$ Check that the center of all of your objects is not off and that there are no animations applied to any rigged characters. $\endgroup$ – Jude Desir Jun 27 '19 at 22:01
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$\begingroup$ Thank you @JudeDesir, it ended up being something else! $\endgroup$ – Jonesnoh Jun 27 '19 at 22:44
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I realized that somewhere in the modeling process, the skin and eye meshes had become very, very slightly rotated. This meant that my mirroring was also rotated.
