Why does Xcode 8 mess up my UI?

I have upgraded to Xcode 8, I opened up my main.storyboard in IB. Everything seemed fine. I then look at my version control and see there are a ton of changes to my main.storyboard file (that Xcode 8 automatically whenever I opened the file). Whenever I go to build and run my app on a device, it is messed up and most of my UI has completely collapsed on each other. But whenever I discard any changes to that main.storyboard file, and run on a device, it's good. As soon as I open main.storyboard, all of those changes come back and mess up my UI. Anyone have ideas what this could be and how do I get past it? Thank you