Multi-cut Tool Breaking my Edge loops

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Hi there!
So I'm having a really big problem with the Multi-Cut Tool. After using it to keep the quads clean for good topology, the edges that the multi-cut tool cuts through causes the edge loops to break and selects the edge below what is supposed to be selected instead? (Please see attached images) Also the faces are broken in these areas and just look incredibly glitchy. When it does this I can't do UV mapping or any kind of textures because it throws the entire geometry off, but my model can't have clean topology without using the multi-cut tool either.
If someone could help me figure out a way to sort this out or if I'm doing something wrong with the tool, I'd be SO grateful - I feel like pulling my hair out at this point.
Thanks!
Katie