Before I begin my question I need to explain specifically what and how rennet is made. Rennet are enzymes scraped from the stomach of an animal, and is used to help give cheese it's texture. So my first assumption was "it's assur because of basar vchalav and non kosher if it's not from a kosher animal." However when I looked at the specifics my mind was thinking otherwise. I found that it can't be basar vchalav or non kosher because it's not an ochel by itself. And it's only used as an additive for texture and not flavoring. That being said, is there a problem eating non kosher-certified cheese other than gevinas akum? If not, what prevents us from using animal rennet in kosher cheese?
The prohibition of eating "Non Kosher cheese" is called "Gevinas Akum". This has nothing to do with Kashrus. Even if all the ingredients are Kosher 100%, one may not eat cheese made by a non Jew due to Gevinas Akum.
See Rabbi Jachter for a complete explanation.