I went to clean my stock air filter on my Rubicon and I noticed there was some oil on it. The whole thing wasn't covered, just where it sits against the piece on the side. The little rectangle filter had oil on it also. Is this normal or do I have a problem?

 

That little rectangle filter is for the crankcase vent. A slight bit of oil there is nothing to worry about.

 

What about the main air filter?

 

How is your crankcase oil level? if it is too high(overfull) this can cause the oil to splash back through the crankcase vent and to your filter.

 

The air filter must be oiled we only use Honda air filter oil (it's colored green)