It's probably either something you said or something she could see in your history that raised some concern but not enough to send you for secondary inspection.

Do you have a history of things like side trips to Mexico or Canada? Have you made a lot of trips for longer than a normal vacation period of a couple of weeks? Is this a business trip or personal? If it's business did she ask you who you were visiting? There are plenty of things that will raise flags, and as airprox says, there's no automatic right to a 90 day stay.