This issue was mentioned with the same title for previous versions of FileMaker. I am experiencing the same:
OS: OS X El Capitan V. 10.11.2
FileMaker Advanced 14.0.4
The curious difference is that I have three different folders with layouts with the same name on each, but just in one folder I am experiecing this issue.
I have created a new folder, moved the layout into it, but the problem stays the same.
Is there any step to avoid this?