Sakura was holding back a secret. Something important, that made her demeanor nervous and jumpy, when Sasuke questioned her. She wouldn't let any information slip about it, wouldn't let anyone in her mind, and the long-forgotten ideas of a sleeper agent were coming back to the surface of medic talk.
Whatever she was hiding, it had to be important, because not anger nor pleads would pry the information loose from her lips. It made her act guilty, fearful, her every action done only after steeling herself to with the utmost resolution. Kakashi knew it had to do with Sasuke and the Sharingan in general.
It could have been trauma. It was a miracle her mind worked at all. Nothing was wrong with her, however. No one could see what was going on in there, and the rest of her body didn't give any clues. No physical torture, no abuse of any kind. She was perfectly fine.
But if she had been, she wouldn't have had those nightmares. Wouldn't react so violently to the Sharingan and Sasuke. Something was off, but it was impossible to tell what.