I think with Gerty, as infinetesimal as the chances were that Sam is telling the truth,
he had to give him the benefit of the doubt.
After having three years of not having anyone around.
as far as Sam's concerned, Gerty is his best buddy,
someone he can rely on and treat like a human being.
When Sam awakes, he has no memories of the crash,
but overhearing the computer AI Gerty(Kevin Spacey)
receive instructions to not let Sam out of the base, he fakes an accident and arrives at the scene of the lunar crash, only to find his doppelganger still unconscious.