I wouldn't worry too much just yet. In case you have any travel plans for Christmas, your wife is a US citizen so she can travel to all EU countries without a visa anyway.
All 4EUFAM cards (for UK citizens' family members) are valid till 31 December 2021, and applicants can use the online system up until that day. All current permissions come with a further auto-extension to 15 January 2022. So there's nothing to worry about for the next 3 months.
I'd just send an email to both
eutreatyrights@justice.ie and
immigrationsupport@justice.ie to ask them to clarify whether this is a mistake now, and wait for their response before taking the next action. (Remember to put all of your details in the email, including but not limited to name, DOB, address, IRP number, passport number, spouse name, spouse passport number etc, so that they can answer your question right away without having to go through further back-and-forth.)
If they don't come back with any satisfactory answers before 15 December 2021, put in a new online application.