When MacGyver throws the coat with the bomb in it under the vehicle, it goes off and a few seconds afterwards, you still see the driver sitting the way she was before it went off. Then she moves out of the way.
The merc plugs the mic into the radio's headphone socket (labeled "PHONES"), instead of into the 4-pin mic socket below it.
When MacGyver enters the wheelhouse on Damien, the wheelhouse is fully lid up.
No boat nor ship would have lights on, on the wheelhouse while sailing by night. As it would be impossible to look outside.
Pete traces MacGyver's phone call to a phone box at Bristol Harbor. There is no such place in California.
The common myth that someone isn't listed as missing before the passing of a certain amount of time, 25 hours in this case, is false. Of course the character might believe it's correct, but working for the Phoenix Foundation she would probably know better.