The initial bug (with the “Cannot create repository version.”) sounds a bit, but not exactly like Issue #8410: syncing deb-repos in pulp 3 fails with "The path for file... overlaps" - Debian Support - Pulp. I will need to check if the error message was changed between pulp versions. If it is the same bug, then that has been fixed in upstream pulp_deb and the fix will be included in the Katello 4.0.1 release.
The other bug you are seeing sounds like Issue #8692: Repository sync will fail if Debian components are defined on the remote - Debian Support - Pulp which was first reported yesterday, and I have not yet had a chance to look into.
I will post again once I know more.