The Mariners last week became the first fourth-tier side in history to beat the English giants in a competitive game in what is one of the biggest stories in the club’s history.
However, the League Two outfit failed to register Clarke Oduor in time for their penalty shoot-out victory over the Red Devils in the second round.
"Odour was registered one minute after the 12pm deadline set the day before the game and Grimsby released a statement explaining the situation which has cost them a huge chunk of money.
"The registration of Oduor was submitted to the EFL at one minute past the deadline, and the issue was not immediately identified by the Club due to a computer problem being experienced at Grimsby.
"We accept the fine imposed and fully recognise the importance of adhering to competition rules and regulations. This mistake was not deliberate, and the Club acted transparently by self-reporting the breach as soon as it came to light.
"Since this incident, we have undertaken a thorough review of our processes and implemented strengthened measures to ensure it cannot happen again."
The match went to a penalty shoot out, and Oduor was the only Grimsby player to miss his spot-kick against United goalkeeper Andre Onana.
The EFL’s board determined the club’s non-compliance was not deliberate, with no intention to deceive or mislead but the punishment was still handed out.
In 2023, Barnsley were kicked out of the FA Cup after fielding an ineligible player in a first-round replay against Horsham, meaning Grimsby’s punishment could have been a lot more severe.