I'm not surprised that Companies House is lagging behind right now. Basically everything is broken because of Covid, I can't imagine non-profit paperwork is at the top of the priority list. I will also say, as someone who has worked most of my professional life in non-profits, government paperwork is the bane of everyone's existence and having some sort of screw up (whether it is your fault or not) is practically a rite of passage.
As Arathorn mentioned in a sibling, we're chasing down our accountants to see if we can get this sorted out, but this isn't a sign of any larger trouble than a paperwork mixup.