Looked at it again with fresh eyes, and I'm an idiot...It looks like the distorted colliders are because the colliders aren't flipping when I flip the sprite (using the FlipX method in code), which I assume is expected behavior. I'm still not sure why I'm getting the error message, but it doesn't seem to be affecting anything at all in my game. I'd be happy to send you my project if you want to still take a look, though.
Also, do you know of a way I could solve the new problem? I can think of a few workarounds, like having separate sprites, or creating a second prefab that is flipped before runtime (clicking Hflip in the inspector correctly flips the collider), but I'm guessing I've missed something simple.