For me, the issues were mostly related to the period of time I started using FreeNAS, and getting a bit too creative with plugins and jails.
On the first part, there was a period of time when the project was going through some upheaval (quite a few years ago now) and I had some issues with upgrades.
This goes hand in hand with the 2nd thing - I was trying all sorts of plugins and using it as a BT and newsgroup client. These did not upgrade well.
I suspect that a fresh vanilla build (TrueNAS now) would probable be zero maintenance. I need to upgrade my drives (a bunch of 1TB drives from the era I built it), and I’ll probably use this opportunity to start fresh.