This question has been asked before on the Net, and there are some who say it happened once in advanced training operations. Unfortunately, I found no detailed reference.
For the likelihood of the events which lead to the ejection sequence, see this question.
The ejection sequence is at least factually wrong when showing both seats being ejected almost simultaneously. In the F-14, first the backseater (RIO - radar intercept officer) would eject, and the ejection of the pilot would happen 0.4 s later.
The ejection system of the F-14 was certified for 0-0 ejection (on the ground and at rest), and the canopy would be thrown backwards by an explosive charge. In a flat spin, a case not anticipated during development, it is possible that the canopy stays trapped in the turbulent, separated flow above the airplane, and then the first seat to come out has a chance of hitting it. At least this detail is not impossible.
Ejection is a violent process, and limbs have been dislocated and/or broken, and pilots have been knocked unconscious during ejection. Hitting the canopy in a still accelerating seat could indeed knock the seat's occupant unconscious.
This was fixed at least so far that a technique was developed to end the flat spin of an F-14. For other aircraft the system is tested and certified with the aircraft at rest, so hitting the canopy in a mid-flight ejection is impossible when the jettison mechanism works as intended. There have been cases, though, where the canopy failed to separate, and then an interlock would prevent the seat from firing. More modern designs use canopy breakers for clearing the way through a closed canopy, but they work only around the head. I don't want to know how the pilot's knees get mangled form the acrylic (or - even worse - the polycarbonate) when it is their time to clear the canopy.