Steps to reproduce:
1. Download and open attached project "repro_728988.zip"
2. Make sure that both DLL files in the root Assets folder are marked as "Editor" only
3. Build for any platform
4. See editor.log file and notice that in section:
"Used Assets and files from the Resources folder, sorted by uncompressed size:
<..>
0.1 kb 0.0% Assets/ThisDLLHasExtraClass.dll"
The file with extra class is included, while in a different section of the log file it says it's being ignored:
"Ignoring 'Assets/ThisDLLHasExtraClass.dll' because we're compiling for WindowsStandaloneSupport"

Notes: Tested for WebGL, Win x86, Win x64, User reported for Android - seems to be platform independent.

Tested on Win10
Reproducible in: 5.0.3f2, 5.1.4f1, 5.2.1p4, 5.2.2p3, 5.3.0b6