Please, let me this contribution.
I had this problem working with Xcode 8.0 (8A218a) and for a iOS Deployment Target 10.
Concretely, Xcode could not read the MapKit.framework. Error message said:
ld: warning: ignoring file /Users/Admin/Documents/APPS/PeekaWish/PeekaWish/MapKit.framework/MapKit, missing required architecture x86_64 in file /Users/Admin/Documents/APPS/PeekaWish/PeekaWish/MapKit.framework/MapKit (3 slices)
The worst thing was that I had not made any changes. The inconsistency apparently occurred after a bad Product Build (My project folder appear duplicated on the Xcode Editor, on Left Side, the Navigator Bar)
I lost a lot of time: linking repeatedly the MapKit.framework
Finally, I found the solution. It is a mix of above solutions.
1 STEP: Click on Product-> Scheme -> New Scheme and just hit OK
On TARGETS (the App) and Build Settings:
2 STEP: Deleting Framework Search Paths (leave these fields empty)
3 STEP: Always Search User Paths -> NO