I opened up the airbox on my 05 Rubicon to check out the air filter. I noticed that the dust cover was pushed inside the breather joint to far. So I pulled it out and it was covered in some kind oil and there was oil inside the breather joint. Should there be any kind of oil inside there? I went ahead and cleaned it out. I did not mess anything up did I?

 

That's the crank case breather, and its normal for it to have oil, there's always oil vapour going up there and sometimes you may get a splash. Should be ok to clean the foam filter, it'll oil up on its own again,and it is usually pushed down into the joint anyway with the foam filter sealing around the edge.

When I installed a K&N on my bike I got an extra peice of air filter foam to cover this opening creating a seal around the edge like stock.