He knew that the human captain suspected something.
The captain suspected that Reed hadn't been asleep when he received the call, as evidenced by the exhausted look of despair on his face.
The captain suspected the doctor was growing bored with the number of stress-related problems caused by their long stint without shore leave.
The fleet's captain suspects a trap, but it seems at first that the New Republic's ships have the upper hand.
The captain suspected that men were hiding under the burqas, too.
The captain didn't suspect how many of his men had died in the difficult maze of Engineering.
McCoy could tell that Jim hadn't anticipated finding the first officer here, and he wondered if the captain now suspected the reason for his visit.
"I cannot believe the captain suspects one of the crew."
I suppose the captain of the Enterprise suspects sabotage.
The captain suspected a lot of Spanish, Chinese, or what-have-you went on in his absence.