You won't need to completely disassemble your build but you will need to remove the motherboard to clear that. It looks like a piece of metal coming from the IO shield, though I'm confused as to why its there in the first place as I believe all of EVGA's IO shields now have cushioned backs rather than those metal clips...

You could just break it off but the proper way to fix it is to take the motherboard out and but it back in making sure the metal peace is on top of the usb port.

Unfortunately, this is part of the IO shield and it basically got caught by the port, you will need to remove the MB and bend it back out of the way.  You want to mount MB's into the IO shield as straight as possible to avoid this problem, as this typically can happen when you have the board partially aligned and are moving the board mainly towards base plate of the case or you are bringing it in at an angle, it is easier to avoid when you are very slightly off of the standoffs and are moving it laterally into the IO shield.
Personally, I mount the board, and if the shield gives me any trouble, I remove it, it really doesn't do that much anyway, it is 90% there for aesthetics, the other 10% is basically to keep dust out, which can also be done with positive case air pressure.

Templar93
Had the same thing happen with my Classified K MoBo. And yeah had to completely remove the board and fold the metal out of the way to clear it. Was kicking myself in the a** for not paying attention.

Did you remove it or just bend it out of the way?  I just removed mine because it didn't seem like it was serving any purpose and none of the other cutouts on the shield had a metal piece like that.

It is not a "manufacturing defect" this is normal and when you install your Motherboard into a case you have to ensure it is installed correctly.
MSI I/O Covers are the hardest ones to set in.
Also the Grounding Tab is not meant to be bent back and forth as you above and that is why it broke off.