Hard to say for sure, but a common penalty is not withholding enough throughout the year. The rules are a little complicated and I don't know anything about CO specifically, but the idea is that you can't wait until tax time and pay the whole thing at once. The state needs your money on an ongoing basis all through the year. The size of the penalty typically is a function of how big the underpayment was.
Again, I'm not certain that's your specific problem, but it is a common source of a modest penalty like that.
