With --ignore-non-existing and incremental recursion, rsync prints the "not creating new directory" verbose message twice for each directory.  This is because directories are visited twice in incremental recursion.  A test needs to be added to only print the message on one of the visits.

$ mkdir src src/subdir dest
$ rsync -r --ignore-non-existing -vv src/ dest/
sending incremental file list
delta-transmission disabled for local transfer or --whole-file
not creating new directory "subdir"
not creating new directory "subdir"
total: matches=0  hash_hits=0  false_alarms=0 data=0

sent 46 bytes  received 16 bytes  124.00 bytes/sec
total size is 0  speedup is 0.00