Frame "will be different at run time".... Isn't that the whole point?
To get rid of the warning, and let the constraints place the views "correctly", just select the view that is giving the warning, press the little triangle thing in the bottom right corner of the storyboard:
And then select "Update frames" for "All Views in Container"
(I wish there was some way of doing this to a whole storyboard. At least I haven't found it)
Select a view and press
- Option + Command + =
This will update the frame size. Repeat for all offending views. It doesn't take that long, especially if you find them by clicking on the error messages.
Thanks to this answer for the idea.
Notes
After updating to Xcode 8, and choosing some View as device, I was getting this error. The menu is different than in Xcode 7, so @Spoek's answer was no longer working. Also clicking Update or Reset was not working for me.
Update
Update Frames now has its own button. That's why I missed it before.
You can change simulated metrics size for example to 4-inch iPhone!
Or Freeform and then change the size to what suits you best.