Tested with latest 2.14.x-SNAPSHOT bin package.
Use the attached sample GeoTiff to reproduce the bug
This bug appears only if JAI-EXT is enabled ( -Dorg.geotools.coverage.jaiext.enabled=true )
and only on layers that defines an InputTransparentColor o OutputTransparentColor ( available on mosaics )
No errors appear in the log.
Download the latest 2.14.x package: https://build.geoserver.org/geoserver/2.14.x/geoserver-2.14.x-latest-bin.zip
Download the attached sample file or use a GeoTiff with nodata values.
Create a GeoTiff store from the sample file
Publish the layer
Check the layer preview: it should work fine
Go back to the layer settings and set the "InputTransparentColor" to 000000
Check the layer preview: the images are bad
The same happens with ImageMosaics that set an OutputTransparentColor value.
Reproduced on Windows (binary package) and Linux (war on tomcat)