Because he's counter intel in the FBI. Suspect everyone
Yeah that and his wife was just fricking with him about suspecting everyone of something a few minutes before that plus the Reagan issuing the order to go after sleeper agents kind of set that up.
I don't get why people think it was unbelievable he suspected.
1. he was a highly trained counter intelligence agent. one can assume he is highly skilled in reading people.
2. upon their first meeting anyone not trained could've seen that phillip (keri Russell's husband) was acting very uneasy once he said what his job was.
3. the high profile case they are currently following is fresh in all their minds and the car in the garage fits the exact description except for the plates. which is why he checked the plates so adamantly.
4. when he asked for jumper cables it was obvious phillip was very anxious when he was near the trunk.
add all these things up and even someone not trained would've at least picked up a little uneasiness