I have had several clients pay their corporation tax in good time only to find HMRC allocating this to the incorrect tax year. Because the earlier year is overpaid a refund is generated automatically and then a reminder is simultaneously sent out stating that the current tax is unpaid. Mind-bogglingly stupid!
The payment counterfoil has the correct reference which includes a suffix to the UTR. Many clients set HMRC Corporation Tax up with their online banking and pay using the UTR as the reference. I know they should use the reference including the suffix from the payment counterfoil, but even when we tell them to use the full reference and it states what to do on the back of the HMRC statement, client apathy sets in, as it does on many things to do with accounting, bookkeeping and tax.
Surely it is hard enough getting tax paid, without HMRC sending it back. It must be possible for a simple programming change to reallocate tax to the correct year without having this nonsense going on.