Colorado law requires that you register in Colorado if that is where you live. If your vehicle plate is Colorado and your trailer plate is Idaho, that will probably bring up some questions if you are stopped. Most cops won't write a ticket just for that, but of course there are the rare few who will write people for everything they possibly can. As far as making you more likely to get stopped, simply having an Idaho plate on your trailer doesn't make you more likely to be pulled over. That alone would not justify a traffic stop. Again the plate discrepancy would be the issue. But keep in mind your rear vehicle plate isn't really visible when you are pulling a trailer, so it really doesn't increase your chances that much.
The fine for such a ticket would be pretty minimal. The only way it could turn really crappy for you is if for some reason the cop decided to tow your trailer, which technically they could do. But that is super duper unlikely based solely on the registration issue. You would have to REALLY earn that tow through other violations and behaviors.