Don't put them together for at least 4 weeks, the sperm need time to die off. If you thought you saw something crawling on another pig at the shelter it's not mites, probably lice or fleas. Mites are microscopic and you can't see them with the naked eye.
Here is some advice from Cavy Spirit website:
-Quarantine means keeping the guinea pigs in two different rooms, which of course requires two separate cages.
-You should handle the new guinea pig last. You should wash your hands after handling the guinea pig. It's a good idea to keep a smock in the room with that guinea pig. That way you have less risk of transmitting parasites or other things on your clothing.
-Examine your new guinea pig very closely and carefully while in quarantine. Look for signs of mites (scratching and hair loss). Mange mites are not visible to the naked eye. Look for lice, fleas, fungus (ringworm). Look for eye or nasal discharge, excessive sneezing, wheezing, loud breathing and more. If you suspect your new guinea pig is not well, please take it to a good vet as soon as possible. Do not delay. Guinea pigs can go downhill fast.