So after a three week RMA with Terasic I learned that the R15 resistor underneath the board was knocked off. I wasn't sure how until it happened AGAIN and I discovered that the USB hub v2.1 comes into contact with it and will scrape it off. Thankfully I was able to find it and resolder it, even thought I don't have the proper tools to solder on that scale, and I'm just glad it works.
I will not be using the MiSTer hub so a external one will have to do. I guess this is another thing that can be added to the list of poor design choices of that hub. Looking online, all the photos I found have different layout on the bottom so it could just be an issue with newer revisions of the DE10-Nano. Maybe it's only the kit I got from the Ultimate MiSTer store, the SDRAM they sent me was faulty too.
Terasic was kind enough to send over a partial schematic so if you're handy you can replace the 100k ohm resistor yourself.
TLDR: Anyone with a newer board revision of the DE10-Nano shouldn't use the MiSTer USB hub, it comes into contact with a resistor on the bottom and can cause damage.