A real-time tweet from a student hiding in Arapahoe High during the shooting:
@patrickstanton: My brother's text w/ my niece while in class at #ArapahoeHigh
A reporter said that one problem that police hadn't anticipated before Columbine were the number of students who hid and where they hid.
While they were trying to clear the school, students began appearing from everywhere. They were coming out of lockers, dropping from the ceiling where they had hidden behind the tiles, and every nook and cranny there was.
In addition, the police had to look in every possible place in case some were too scared to come out. This made clearing the building a much more fluid and difficult situation to handle. Knowing it can occur with huge numbers of students helps deal with it, but it's not easy.
I can imagine that with fear and massive amounts of adrenaline, students would be able to hide in seemingly inaccessible places.
In addition, some parents were not happy with the students being patted down after leaving the school. However, most of them understood why it was necessary.
Edit to add: Many students said they were following Twitter while in hiding. It gave them immediate feedback from many sources.