Hi @lindyjcooper
This happens here quite often too.
Personally, I don't like the idea of an Exception Report - or adjustments to VAT Return for that matter. I much prefer to have everything as simple as possible - so I will always enter missed invoices as though they were dated the 1st day of current VAT quarter (with a Memo to show the Actual Date).
As long as you aren't talking about £000s of VAT the VATman won't be too concerned.
(after all, this is VAT you should/could have reclaimed 3 months earlier)