which version of dh_python3 did you use? Can you paste -v/--verbose's
output?
This is an up-to-date sid schroot (at least it was up-to-date yesterday). Not sure if this output helps, except for it saying "moving files from debian/python3-kombu/usr/lib/python3.4/dist-packages to debian/python3-kombu/usr/lib/python3/dist-packages/" two times.
It seems to move the files ok, but leave the directories behind. Which is weird, I haven't seen this happen before with any other package.