As of coreutils 5.92, there is a regression over previous versions:

$ rm -rf /tmp/test$$
# this fails:
$ mkdir -p /tmp/test$$/new/.   
mkdir: cannot create directory `/tmp/test12097/new/.': File exists
# it works however if the directory exists
$ mkdir -p /tmp/test$$/new/.    # now works as new exists

The first mkdir -p command shown used to work with older coreutils, and there is no reason why it should fail today.

See also SourceForge Bug #1336030 in the leafnode package,
https://sourceforge.net/tracker/index.php?func=detail&aid=1336030&group_id=57767&atid=485351