Stephen,
apologies for the late response - I've been out sick last week.
I've poked around a bit in old bug reports and the only thing I could find is
https://tickets.puppetlabs.com/browse/PDB-1812 , which says that PuppetDB 3.0.2 fixed an issue with autovaccuming that was not properly garbage collecting space in postgresql.
If you're on a version even older than that, and can't upgrade, it might make sense to look into manually configuring some regular database maintenance. That could possibly limit the growth of the files on disk to what the database actually needs for it's day-to-day work.
Good luck, David