Error in Annual Return

Client submitted own first annual return online to Companies House and on seeing a copy I queried the 1000 shares (100%) allocated to himself. On incorporation he only subscribed to a single £1 share. He is the only share holder and it is his own one man company. He was surprised and clearly he had made an error completing the return as he had not consciously issued a further 999 shares. On my advice he contacted Companies House and they assumed he had simply issued the remaining shares. He is not bothered provided there are no consequences. He has not paid for the shares.

Comments would be welcomed on the implications of this and whether in fact no harm has been done and can it be left as is or can and should it be corrected. In the former case I assume the accounts should agree with the Companies House record even though this was not intended. Thanks in advance.
Stephen Quay