I'm afraid my understanding of commercial in this case is different to yours, @Marion818. The commercial condition that often applies with planning permission (such as yours) means the converted building cannot be used to deliver a profit/yield. It's for own use only (like a granny annexe for instance) and is (partly) there to stop 'bed in a shed' type activities.
The 90 day limit doesn't really come in to it; your listing would be commercial from a planning perspective IMO (because you're making cash from it) with or without adherence to the 90 day limit.
Without more detail, I'd say the email from your council is about the planning permission, not the 90 day rule, the latter of which can only be fixed with change of use PP (akin to finding a rollerskating unicorn on Muswell Hill Broadway). If you did manage to get permission, separate dwelling issues might then crop up (additional council tax etc).
Sounds like a 'friendly' neighbour has had a chat with the council?
Your listing looks like a cracker and I hope you're able to find a way through this.