here's the testcase:
  cd ~/
  rm -rf test x
  mkdir -p x/test
  touch x/test/{1,2,3}
  cd x
  sftp localhost <<<'put -r .'

with openssh-6.7 and older, you'd get:
Connected to localhost.
sftp> put -r .
Uploading ./ to /home/vapier/.
Entering ./
Entering ./test
./test/3   100%    0     0.0KB/s   00:00
./test/2   100%    0     0.0KB/s   00:00
./test/1   100%    0     0.0KB/s   00:00

starting with openssh-6.8, you get:
Connected to localhost.
sftp> put -r .
Uploading ./ to /home/vapier/.
Entering ./

and nothing is actually uploaded.  the failure is due to the remote doing mkdir(/home/vapier/.), getting EEXIST, and then returning an error to the client which makes it stop.

bisecting the public github repo shows the first bad commit is this one:
https://github.com/openssh/openssh-portable/commit/7d845f4a0b7ec97887be204c3760e44de8bf1f32
(i had to cherry pick 0cdc5a3eb6fb383569a4da2a30705d9b90428d6b and 83b9678a62cbdc74eb2031cf1e1e4ffd58e233ae to get it to build)

its parent obviously works fine too:
https://github.com/openssh/openssh-portable/commit/139ca81866ec1b219c717d17061e5e7ad1059e2a

it might be that the new one is doing more error checking, but it seems like the server or client should handle EEXIST correctly.