Fortunately, Colorado has pretty comprehensive animal laws concerning pet stores and luckily, it covers guinea pigs. Pet stores in Colorado must be licensed and if they do do comply with the animal laws, they can lose their license to do business or be fined, depending on conditions.
I would file a complaint if I were you. You don't have to feel helpless. If you make a complaint, it will be investigated:
"§ 35-80-110. Inspections--investigations--access--subpoena
(1) The commissioner, upon his or her own motion or upon the complaint of any person, may make any investigations necessary to ensure compliance with this article."
Anyhow, here is something you may wish to consider - Colorado law states that any animal in a pet store that is sick or suffering must be provided vet care in a timely manner or euthanized by a vet humanely. They require adequate and appropriate living conditions and are very specific on size and type. They are also specific on breeding of animals for sale.
You can find the complete Colorado pet store facility laws and process for demanding an inspection here:
Agriculture-Colorado:Pet Animal Care Facilities Program - Click on "PACFA Rules & Regulations".
You can also find the information for filing a complaint here: Agriculture-Colorado:Animal Neglect or Cruelty
Additionally, here is the The Colorado Federation of Animal Welfare Agencies:
Colorado Federation of Animal Welfare Agencies. They may be able to help or give you advice if you tell them what you saw.
I would also contact your local humane society and ASPCA. The more people you make aware of the situation, the easier it will be to correct the issues at hand. Even if they are unable to do something directly, you can ask them if they can steer you in the right direction. The right information can be so easy to get if you ask for it. Contact your local animal welfare organizations as well and let them know what is happening.
One more note - supporting pet stores that do not sell live animals is so helpful and will really give you a sense of responsibility knowing that your dollars are not going to supporting the inhumane conditions found in so many pet stores, but rather to a pet store owner who sees animals as more than a profitable product. I know you enjoy looking at the animals, but do you really want to put yourself in this sort of agony and guilt again?