Ah.  I didn’t fully specify my test case, sorry about that.  In reality I did mkdir ~/test; touch ~/test/{a,b,c,d} .

Looks like that’s the key though.  If the first file in the directory to be copied is a normal file, not a directory, the call fails. So

mkdir ~/test
touch ~/test/{a,b,c,d}
path/to/emacs -Q -batch -eval '(copy-directory "~/test" "~/a/new/directory/" t t t)’

will fail, but

mkdir -p ~/test2/a
touch ~/test2/{b,c,d}
touch ~/test2/a/e
path/to/emacs -Q -batch -eval '(copy-directory "~/test2" "~/another/new/directory/" t t t)’

will succeed.

I've replicated the former behavior on Fedora 26, on a clean build of the most recent master (bc511a64f6). M-x report-emacs-bug template for that system is attached, along with the strace output.  There are no references to mkdir, unfortunately.  It seems like the issue is that copy-directory never actually calls make-directory in this case.  If neither condition in the middle cond block (list/files.el#5543) applies (which seems to be why this only happens with a NEWNAME with a trailing slash, and non-nil COPY-CONTENTS) then copy-directory just proceeds to the dolist, and if the first item is a file, it goes straight to copy-file, which then fails, as the target directory doesn’t exist.

Looks like the issue may have arose in commit e22794867d878d53675fcc91d2ef1ad2494a2ff2, trading file-directory-p for directory-name-p in the first first condition in that cond block.

Would adding a condition like:

1 file changed, 3 insertions(+), 1 deletion(-)
lisp/files.el | 4 +++-

modified   lisp/files.el
@@ -5541,31 +5541,33 @@ into NEWNAME instead."
 	    newname (expand-file-name newname))
 
       (cond ((not (directory-name-p newname))
 	     ;; If NEWNAME is not a directory name, create it;
 	     ;; that is where we will copy the files of DIRECTORY.
 	     (make-directory newname parents))
 	    ;; If NEWNAME is a directory name and COPY-CONTENTS
 	    ;; is nil, copy into NEWNAME/[DIRECTORY-BASENAME].
 	    ((not copy-contents)
 	     (setq newname (concat newname
 			    (file-name-nondirectory directory)))
 	     (and (file-exists-p newname)
 		  (not (file-directory-p newname))
 		  (error "Cannot overwrite non-directory %s with a directory"
 			 newname))
-	     (make-directory newname t)))
+	     (make-directory newname t))
+            ((and copy-contents (not (file-directory-p newname)))
+             (make-directory newname parents)))
 
       ;; Copy recursively.

Impact the current security concern?

Andrew