No, I don’t know of any bug.
We do put a “hold” on the freedombox package when installing apps. This is to avoid any situation that would cause freedombox package to be removed (e.g. due to package conflicts in testing/unstable).
However, it’s not clear to me what actually solved the problem here: the “unhold” or the “full-upgrade”.
Also @Clearmask, can you remember (or check logs or command history) what happened or was done before the upgrades stopped working?
To be honest, they may never have worked. I assumed it was auto updating over night as I think I had read somewhere that it did that, but I don’t recall ever seeing any indications anywhere in the GUI that it had been successful until now. I suspect I’ve just been using the version it shipped with until this update.
When I tested the stable image, the updates didn’t work either. But the error seemed different. (The problem @Peterc was checking, and that is supposed to fix itself after a day or two, but I used the workaround.)
But this issue and test did not cover your case. 
So, if you feel like checking for your case, I guess you could backup your sdcard, or use another one, to see if you see the same problem again when booting the stock image.