Client suffered the problem with HMRC's intermittent error on RTI submissions whereby they record the wrong figures so the employer is recorded as owing more PAYE & NI than they actually do. There is an earlier thread on this with various comments from people saying that it takes over a year for HMRC to sort it out. This has happened with Moneysoft submissions =- don't know if it has also happened with other software.
My client's problem became obvious very quickly as an employee got a letter from Universal Credit saying he was no longer entitled to anything as he earned so much per month. He got in a flat spin & I advised him to contact the Universal Credit helpline with his payslips & bank statements & surprisingly enough he got his problem sorted out very quickly & they admitted they had the wrong figures at their end (this does rather suggest that it happens quite often). This didn't feed back to HMRC who show quite a chunk still owing by client for month 2 payroll after the client paid the correct amount (correct amount per their own payroll).
I phoned the HMRC online helpdesk yesterday as per Moneysoft advice and got someone aiming for worst employee of the year who basically refused to do anything at all & firmly said they can't do anything. Phoned the Employers Helpline this morning & got someone very helpful who said they prefer to see if it will get sorted out by the next month's submission, ( i.e. they don't want a repeat submission of Month 2 by the client) but they have put a note on the employer's record - we had quite a discussion about the Universal Credit situation as evidently the HMRC staff member had received a similar call about this before so he was pleased to hear that UC had sorted it out so quickly.
Since my call, the employee with the problem has forwarded a tax code that he received after his worrying contact from UC. This shows that the problem is with HMRC as they have clearly set up a duplicate employment - - so apart from sticking a large lump adjustment to reduce the code for estimated tax you owe this year, they have down how the remaining tax free amount is used and the remaining small code amount goes to the employer & then there is a second employment with the same employer shown as getting no tax free pay with a BR code. I will call the employers helpline tomorrow at 8am with this detail & hopefully this can be properly sorted without taking a year.