The company issued an apology to its customers but has not paid any compensation for its error.
A spokesman for the company told Independent.ie that less than three per cent of its 65,000 residential clients had been affected.
The affected borrowers had originally taken out loans with the Bank of Scotland (Ireland), which ceased operations in 2010, and are now being administered by Pepper.
Pepper misstated the number of missed payments its customers had to the Central Bank’s new Central Credit Register, with most cases indicating there were three missed payments when it had been two.
The company said the incident was related to a “processing error” but had since been corrected.
Mortgage Solutions has contacted Pepper for comment.