Mine went through smoothly - my wife was a bit surprised how low it was, but of course, my profits are low too. This is keeping my tax down so I've had the benefit of lower tax and NI for many years - I can't expect to get benefits when I've contributed less, so it seems fair. Lots of small businesses use the allowances to keep profits down, so all seems pretty fair for me.
On the topic problem, I don't understand how an accountant could have produced payslips, and deducted tax and NI for a person self-employed. Surely this is accountancy class week one stuff? It does of course mean that your accountants firm is probably large, and they know your name on paper, and that's why I moved from being a tiny business in a big firm to a small accountant who knows my voice on the phone.
Based on what you say, I suspect their PAYE department has you on the pay list and the accounts department have you as self-employed and they've messed up big time. With a large firm, they'll have the resources to sort this out.
What's the betting they've ot you being paid under the old Ltd company! It does mean they have NOT represented your interests very professionally.