I hate to admit it, but I am stumped.
I've looked through our database of bugs and haven't found anything concerning non-planar faces appearing after scaling a face.
Some other ideas to try:
1. Reset everything to Maya's default, so grid size, or world size, camera settings, etc.
2. Update video drivers
The silver lining with all this I think is that non-planar faces are not necessarily bad. Non-planar faces can be smoothed, rendered and all the modelling tools should still work fine.
Non-manifold geometry is the thing you need to avoid since Maya's modelling tools will give unpredictable results. You can learn more here: https://knowledge.autodesk.com/support/maya-lt/learn-explore/caas/CloudHelp/cloudhelp/2015/ENU/MayaL...
If I learn of anything new I'll update this thread. Or if you find the reason it's happening, please let us know.
Regards,
Carlos