When the FBI agent states that no one is in the house they checked at the end of The Silence of the Lambs, Jack Crawford looks worried and says Clarice's name, as if he's concerned about her safety. How would he know that she was in danger? She was just looking for clues to link Buffalo Bill to Bimmell, right?
While this appears to be a story hole, the fact is, Clarisse has out-smarted Jack Crawford a couple of times, and has proven to be insightful. When Hannabel tells her to 'look inside yourself', she correctly deduces that 'Yourself' is the name of a storage house, and she goes there and looks inside. She also has the insight when Jack speaks to the other officers at the morgue, when they are examining the body of the girl, that he spoke to her in a demeaning way, and it set a bad example for the other men. Then she had the insight into the fact the killer is using the girls to make a suit of their skins, she may have acted on this. He can assume she is ahead of him once again, and has correctly interpreted information she had, and acted on it. While he has no direct evidence she is somewhere else, it is a logical assumption, given her past history, and given the fact he incorrectly interpreted the info he had.