You don't have any problem really.
At worst, your ex has claimed TRS he wasn't entitled to, but that would be a matter between himself and Revenue... of course if they cut off his TRS it will mean an increased mortgage repayment for you, but you must be nearly finished with TRS by now anyway based on the timeline you outlined.
In any case, they have only asked you about your entitlement to the Lone parent tax credit, so that's all you need to answer them on (or did the correspondence from Revenue mention joint mortgage / TRS?) - it is unlikely your ex will come under any scrutiny as he is not working and therefore not claiming the credit...