I got an invidia o2 housing and I can't put the 2 nuts back on the bottom as the housing is too big and will not allow me to fit them around. Will this cause any issues if I do not put them back on?

Remove all bolts. And seperate housing from turbo and install nuts before bolts.

If i understood correctly. The nuts are hitting the housing? So if you seperate it and make the studs become short it will dive you that extra room.

Correct. The nuts hit the housing.

Like i said remove remainding bolts and back off housing and start nuts. Yes it will cause an exhaust leak. Eventually. In time the exhaust gas will eat away the gasket.