I have found a strange behaviour with 'list.files' (it can easily be bypassed with the 'pattern' argument but doesn't seem to me very constistent to the 'files.all' one):
The problem is that Windows files begining with a tilde are returned by list.files, even if they are hidden.
I reproduced the behaviour, opening an existing document 'Test.doc' with Microsoft Word. The result is then:
 "~$Test.doc" "Test.doc"
Under the Windows explorer, the first file appears only if the hidden files are made visible, and the actual name that is displayed is ".~lock.Test.doc#" (another strange thing)
Such files seem to be temporary ones and are not specific to MS Word and it appears that some of them survive to the closing of their application.
R version 3.3.3 (2017-03-06)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1