I've only done a little Ubuntu packaging, but have never really had a problem communicating with upstream Debian maintainers.
I wouldn't call all the packaging differences between the two distributions problems, since in many cases the best you can do is aim for eventual consistency.
For example, Debian might be frozen to the point where it won't accept certain package changes, but those changes are required by Ubuntu. That might show up as a difference in the two releases, but the change may get merged after the freeze is lifted. The same can happen in the other direction.