Headcanon: Of all of Thor’s friends … it’s Fandral who has never truly been unkind to Loki, even after everything that’s happened. I’d like to think that while the others reluctantly accepted Loki into the group for Thor’s sake, it was Fandral who made an effort to be a true friend and genuinely liked Loki’s sense of humor, astute observations, and (only known between them) taste in Asgardian attire. More than once did Loki coach him in how to spin words to win the attentions of women, and he hasn’t forgotten that the trickster god had a lighter, kinder heart once.
And while Fandral might have reservations trusting Loki, he does not pass judgment on business that isn’t his. Instead he downplays a rather sore topic, and teases Loki’s less-than-dignified landing on the skiff. It is the same kind of jest he had always offered to lift the mood, particularly when the others had been too harsh or too critical of Loki for one reason or another already.
In happier times, Loki would banter back and feel more at ease with himself. To see that Fandral hasn’t changed takes Loki aback, and so he says nothing. Being who he is now, there is nothing to say to a man who has always treated him justly.