I had a similar problem on the fork of a Dahon bike.
First: make sure, really sure, that the problem isn't the wheel or any other thing.
If you're really sure the problem is the dropout na dthe dropout is made from metal instead of carbon, you can use a small file on the dropout (it's what I did on the mentioned Dahon). But DON'T FILE 2mm of it. The distance between the dropouts is less than the wheel diameter, so you'll be ok with a fraction of that. Go slow, really slow, and mount the wheel repeatedly to check how it's coming during the process.
If the dropout is made of carbon, I wouldn't dare to file it..