I have not been able to reproduce the problem here, but I can see how it might happen. I opened https://redmine.pfsense.org/issues/9582 to track it and committed a fix: https://github.com/pfsense/pfsense/commit/45f95753963e497b5ce14493f9cca05336d75c7b
You can install the System Patches package and then create an entry for 45f95753963e497b5ce14493f9cca05336d75c7b to apply the fix.
Alternately, you can use viconfig to edit the config and remove that <vlans></vlans> line, or download a backup, edit it out, then restore.