In the movie it's implied that it was a swipe at the sitting PotUS, with the NASA director apologizing to the President over the phone.

In the book it's different. Here's the full quote of the conversation between Mark & Venkat (aka Vincent):

[11:18] JPL: Mark, this is Venkat Kapoor. We’ve been watching you since Sol 49. The whole world’s been rooting for you. Amazing job, getting Pathfinder. We’re working on rescue plans. JPL is adjusting Ares 4’s MDV to do a short overland flight. They’ll pick you up, then take you with them to Schiaparelli. We’re putting together a supply mission to keep you fed till Ares 4 arrives.

[11:29] WATNEY: Glad to hear it. Really looking forward to not dying. I want to make it clear it wasn’t the crew’s fault. Side question: What did they say when they found out I was alive? Also, “Hi, Mom!”

[11:41] JPL: Tell us about your “crops.” We estimated your food packs would last until Sol 400 at 3/4 ration per meal. Will your crops affect that number? As to your question: We haven’t told the crew you’re alive yet. We wanted them to concentrate on their own mission.

[11:52] WATNEY: The crops are potatoes, grown from the ones we were supposed to prepare on Thanksgiving. They’re doing great, but the available farmland isn’t enough for sustainability. I’ll run out of food around Sol 900. Also: Tell the crew I’m alive! What the fuck is wrong with you?

[12:04] JPL: We’ll get botanists in to ask detailed questions and double-check your work. Your life is at stake, so we want to be sure. Sol 900 is great news. It’ll give us a lot more time to get the supply mission together. Also, please watch your language. Everything you type is being broadcast live all over the world.

[12:15] WATNEY: Look! A pair of boobs! -> (.Y.)