You might have hit the B-button during evolution. Pressing the B-button during evolution startles the Pokemon and cancels the evolution. If you're absolutely sure you didn't, was it holding Everstone? Everstone prevents evolution of any Pokemon.
If neither, you might have had a glitch. It's possible. I've done a bit of research, and can't find any instances where a Fraxure evolved at level 49.
But at least it evolved, right?