The Financial Conduct Authority received 1,335 notifications of inaccurate transaction reporting under the Markets in Financial Instruments Directive (Mifid II) in 2018.
The figures have been published by regulatory consultancy Bovill as a "snapshot" into how companies adjusted under the directive in its first year.
Obtained under a Freedom of Information request, Bovill said these figures only represent the companies which were aware they breached the new reporting requirements and thus reported themselves to the regulator.
As such, the consultancy suggested there are likely to be "many thousands" more unknowingly submitting inaccurate reports and are therefore not reporting inaccuracies to the regulator.
Under Mifid II a transaction report is data submitted to the FCA that relates to a financial market transaction and includes details of the product traded, the firm that undertook the trade, the trade counterparty, the client, and elements such as price, quantity and venue.
The FCA uses this information to supervise firms and monitor for market abuse. It also shares some data with external parties, such as the Bank of England.
A number of recent high-profile cases have seen the regulator crack down on companies which did not adhere to the reporting rules, with Goldman Sachs International receiving a £34.3m fine and UBS AG a £30m fine in March.
Damon Batten, managing consultant at Bovill, said: "These results show a substantial number of the 6,000 UK firms executing transaction reports are falling foul of the more complex requirements of Mifid II.
"And these are just the firms that had done their homework and were ready in time for the new regime.
"Given how common reporting errors are among firms that are MiFID II-ready, companies that haven’t detected any should be wary.
"Unless they’re confident it’s because they have Rolls-Royce processes in place, it’s more likely a sign those processes aren’t fit for purpose."
Mr Batten said the regulator would not punish companies for making reporting errors, but would penalise those which cannot identify and report mistakes properly.
If companies are taking it upon themselves to catch and fix their own faults, Mr Batten said, the regulator will consider "all is in order".
He added: "As such, it isn’t the end of the world for firms that might have been unwittingly breaching the regulations.
"But time is of the essence for them to fix things and demonstrate they can clear up their own messes and prevent them from happening again."
The FCA has been approached for comment.