They could have been pick up from the streets or someone could have brought them into the shelter. I am sure that they are other reasons too.

Most likely the reason for the URI(Kitty Cold) is probably from the shelter. It is very common for a kitty to have a cold comming from a shelter. The reason is that it is highly contagious and no matter how hard the shelter tries, it is genally picked up by a kitty and passed around. Luckly it is generally not hard to treat, but very hard to get rid of once it is in a group of cats they all share.