Steps to Reproduce
$ echo "I'm just some text" > ~/Desktop/plain-old-directory/humble.txt
$ bagit validate ~/Desktop/plain-old-directory
true
$ ls -al ~/Desktop/plain-old-directory/
total 24
drwxr-xr-x 6 myname staff 204 Oct 10 21:24 .
drwx------+ 27 myname staff 918 Oct 10 21:21 ..
-rw-r--r-- 1 myname staff 107 Oct 10 21:24 bag-info.txt
-rw-r--r-- 1 myname staff 55 Oct 10 21:24 bagit.txt
drwxr-xr-x 2 myname staff 68 Oct 10 21:24 data
-rw-r--r-- 1 myname staff 19 Oct 10 21:24 humble.txt
I'd expect this to not turn a previously non-bag directory into a bag.