From what I've read here, you're covered. The student lied to you if I understand correctly. You signed him off based on what you saw and understood. It's not your responsibility to call FSS every time to verify that your student actually called. After he gets in the air, it's really on the instructor who signed him off to begin with. The only thing you did was verify his planning.

You did the right thing by filing an ASAP. I would say you're covered and wouldn't worry about a violation. If anything the student and his primary instructor will receive the reprimands.

Just my $.02