If the dogs can follow their scent anywhere, why not up to the trunk? The only thing I can think of is that they didn't get in there of their own accord, but were carried and placed there after the dogs had already searched around the car. Their scent wouldn't be on the ground to follow.
I can't think of any other explanation.
I agree with you. The human scent has to be on the ground in order for the dogs to pick it up.
Ever own a dog?
Then you know that they aren't perfect and make mistakes from time to time.