Water coming out of catch can?

[Slow6]

Ok so Ive been having issues with the new engine with a cylinder three misfire code. Well yesterday I popped the hood and decided to drain the oil catch can on the passanger side valve cover to see how much oil was being pulled out of the crankcase. I dropped the lever and was very surprised at what I saw. In 2k miles I had about a cup of water with a yellow film come out and it smelled like oil and gas. I havent been watching the coolant level since the engine was reinstalled but was wondering what could have caused this? Head gasket leaking? If its being caught in the catch can does that mean theres water in the oil pan and the water vapor is being pulled up into the catch can and water being pushed into the bearings?

Just curious if this could be causing my misfire or hurting my new engine.