It is not currently possible to disable that warning, see discussions on Issue 20397:
That warning was added, because the Windows filesystem does not have
an option to mark a file as 'executable'. Building a linux image from
a Windows machine would therefore break the image if a file has to be
For that reason, files are marked executable by default when building
from a windows client; the warning is there so that you are notified
of that, and (if needed), modify the Dockerfile to change/remove the
executable bit afterwards.
In a sense this also means it's practically impossible to actually solve the issue.
What maybe can help a bit is moving the error message from stderr to stdout, released in docker 17.04. See Issue 29856.