I have a 2013 mcs, i have a check engine light, but my cars runs fine so I don't think much of it, but when I plugged a code reader into it, it would just give me error on the code reader and wouldn't read any codes.
Has anyone else seen this before or know any possible fixes?

 

Probably a BMW specific code. You'll need to take it either to the dealer or a Mini specialist to pull the code.

 

As AZdsrt said or the light is not a CEL but a service engine or service something light.

My experience is a code reader even if it encounters a manufacturer specific error code can decode it and should know it is manufacturer specific. The code will be displayed but the reader won't be able to offer any "help" on what the code means.

Regardless it appears for whatever reason your code reader is not able to handle this condition so you'll need to follow AZdrst's advice and have the code read/interpreted by either a Mini tech at a dealer or at an indy shop.