I ran into this problem recently creating a new project and adding some pods (AlamoFire specifically) to the project. Troubled with it a couple hours or so recreating the project (it was new) several times. Tried all the methods here and no luck.
Eventually I figured out that it was because XCode V10.1 was also opening the old project file along with the new pod-created workspace when I opened the workspace via command line "open myProject.xcworkspace" when I reopened the project after doing "pod install"
Closing all projects before exiting XCode before I did my "pod install" fixed everything for me.