This is a known problem. I’ve had it myself, intermittently. I’m confident that this will eventually get fixed.
Yes, this is an unfortunate aspect for non-technical users. The GUI update app sometimes doesn’t work whereas the “same” commands at the shell work fine. I usually update from shell anyway, so not a drama for me personally.
In some respects Purism would be better to link the GUI update icon to a two line shell script until the GUI update app actually works reliably.