PuppetDB’s bugs and feature requests are managed in Puppet’s issue tracker. Search this database if you’re having problems and please report any new issues to us!
Puppet resource types can “autorequire” other resources when certain conditions are met, but we don’t correctly model these relationships in PuppetDB. (For example, if you manage two file resources where one is a parent directory of the other, Puppet will automatically make the child dependent on the parent.) The problem is that these dependencies are not written to the catalog; the Puppet agent creates these relationships on the fly when it reads the catalog. Getting these relationships into PuppetDB will require a significant change to Puppet’s core.