I had similar issues, until I realized that the problem was with my MAT table not being setup correctly. Fully warm up the car and make adjustments to your MAT table until everything is reading where it should be without using Autotune. Do this for a few days, and then when you are confident about your MAT corrections, start WUE tuning.

Don't forget that you can always right click on the graph and revert the changes if you don't like them.