Mesh deforms incorrectly during stretch/squash animation

I created a rig with a squash and stretch according to the directions in this video https://www.youtube.com/watch?v=Ip-5PD3aNIg

I then animated a simple jump using the character. After importing the character, the mesh did not deform as expected. I have posted an image below of the character at the same frame of the animation in maya on left, and unity on right.

Does anyone know how, or why this happens and how to fix it? Is this a bug a should report to unity?