A procurement system has cost Kirklees Council an extra £60,000, according to an internal report.
The council's scrutiny panel found Marketplace, its electronic buying system, was "cumbersome and ineffective".
Suppliers upload their own invoices, but medium-sized suppliers are often unable to submit theirs.
As a result the council had to contract another firm, Documetrix, to input the invoices at a cost of £60,000.
The problem relates to the size of the files suppliers are allowed to upload - either single invoices or large files.
This is not a problem for small suppliers, which send in single invoices, or large firms which can create larger files, but causes issues for medium-sized suppliers.
Even once the documents are sent to Documetrix, "evidence shows that about 40% of the invoices... have to be referred back to the council because of some discrepancy," the report says.
Kirklees Council is due to meet on Tuesday to discuss the findings of the report and possible changes to the Marketplace system.