I'm not an experienced Illustrator user, but whenever I use pathfinder to combine a few shapes together, Illustrator would create a whole bunch of what appears to look like outlines of every shape and thin thin hairlines that doesn't show up on my art board when I turn on the visibility. I can only see them when I look at the layers on the side. It doesn't seem to make a difference to my art when I delete all of those shapes. Can someone tell me what these shapes are and if it is alright to just delete them?
The paths are useless, delete them.
A relatively quick fix:
Use Pathfinder (or Image Trace, or whatever function that is creating useless extra paths).
Optionally, double-click to enter isolation mode (If there is nothing else in your document don't bother, otherwise this prevents you accidentally deleting something unrelated).
Select one of the invisible paths.
Select → Same → Fill & Stroke (or use the Select Similar Objects button in the options bar)