Need a little more info to to tell you what I think the best course of action would be.
Is it a production folder, and what kind? Really, if its from a reputable company, or pretty much any custom knifemaker you should be able to contact them and they should make it right.
If its a linerlock, one thing you can try is to open the knife and then bend the blade towards the side it rubs when its closed. Don't force anything, or try to actually "bend" the blade but put some stiff side pressure on and see if that pulls things into alignment.