Steps to reproduce:
1. Create new Unity project
1. Import attached "dummy.dll" file for Windows or "MacURI.bundle" file for MacOS
2. Select imported plugin (make sure Any Platform is disabled and Include Platforms Editor and Standalone are enabled in Import settings)
3. Disable all checkboxes in PC, Mac and Linux Standalone Platform settings (x86 and x86_x64 for Windows, x64 for MacOS) and Apply
4. Disable Standalone and Apply
5. Enable Standalone and Apply
6. Go to File->Build Settings and build standalone player
8. Check included plugins in build (Build_Data/Plugins for Windows, Contents/Plugins for MacOS)

Expected results:
Plugins that were specified to be included in Standalone are copied to the Plugins folder in Standalone build
Actual results:
Plugin is not copied to the Plugins folder in Standalone build

Reproduced in: 2018.2.0a3, 2018.1.0b10, 2017.3.1p3, 2017.2.2f1, 2017.1.3p2, 2017.1.0a1

Workaround:
-Disable all checkboxes in PC, Mac and Linux Standalone Platform settings and Apply
-Enable all checkboxes in PC, Mac and Linux Standalone Platform settings and Apply