I've had this in both Xcode 9 Beta 2 and 3.
Whenever I drag a framework into the project or use the '+' buttons to add a linked framework, Xcode moves the referenced file into the root of the project, then adds a reference into the project Navigator that refers to the original location of the framework.
I then have to go and moves the frameworks back into their original location to get the project to compile again.
I can't figure out why it's doing and can't find a way to get Xcode to behave as it should. Any ideas?