There are two points about those.
First, that it is impossible to make cell phone calls from the altitudes the planes were flying. And even if at a lower altitude the aircraft moves too fast to keep the signal connected (moving too quickly out of range of one mast to another). The in-flight phones operate on a different system.
Second. The allegation is that the calls were rigged in advance by recording the phone calls of pre-selected individuals (as the NSA has now been revealed to do on a regular basis), then stitched together to make the calls and leave messages. This has been shown to be very technically possible.
Up to you if you believe it.