I’m doing the character modeling course, and for some reason, the mirror modifier is doing some weird thing, where it works almost everywhere, but in just a few places it doesn’t. It’s especially around his nose, and when I join the body and head retopology, it looks even more messed up. Face orientation looks fine, I’ve applied scale and rotation, I can’t seem to find any issues, it’s just weird.
Before joining the meshes:
After joining the meshes:
In Edit mode after joining:
The object isn’t truly cut down the center, and is causing overlap. Make sure the center of the object and the objects origin is at world 0,0 position (shift S and click cursor to world origin, shift A set all transforms, right click and set origin to 3d cursor) – all in object view.
Also, the mirror modifier should have the clipping / merge (depending on your version) enabled, this will cause the center to never overlap even if you TRY to do it.
Last thing you can try if its still doing it is taking the mesh with the modifier on it and moving it away to pull that overlap apart.
Enable both
Moving the edges back over…
Mirror modifier reflects OVER the object origin, so its very important to work DIRECTLY over the origin. Hope that helps 
Very well spotted and explained.
I would check things as @Kimset said, but just in case, do you have any shrinkwrap modifier applied after mirror?
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