Tried on Ubuntu 17.10, Windows 10 and OSX 10.11.6
Broken: version: 2.79 (sub 1), branch: master, commit date: 2017-11-27 15:57, hash: 2bf38257112, type: Release
build date: 2017-11-28, 01:19:29
Also in latest builds as of 2018-01-18.
Short: Disabled Renderlayers still get saved (blank image) through File Output Node when connected to Composite Node (overwriting previously rendered Images).
I made a test .blend ...