self assessment penalties

Apologies if everyone already knows this - I spoke to HMRC this afternoon about a hand delivered return and was warned that, due to the new systems they were using, any manual return received but not yet dealt with will not be logged untill it is processed, but it will have been date stamped so should be logged in then with the correct date.
This means, according to the officer I was talking to, that penalties will automatically be issued - but don't worry, once the return is processed showing the correct date it will disappear again.
There is apparently no way to prevent this happening
I take it this is the new LEAN procedure
marion hayes