Lyon accused West Ham of showing a "profound lack of respect" after Algeria international Saïd Benrahma's proposed transfer to the French club initially collapsed before being completed a day later owing to the French club's successful appeal to FIFA.
Lyon said the Premier League side did not attempt to carry out the steps needed on world football governing body FIFA's transfer matching system for the deal to go through on Thursday before the end of the January transfer window.
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"Following this incomprehensible behaviour... the international transfer certificate could not be requested before closing time," Lyon said in a statement before the deal was ratified.
"Olympique Lyonnais deeply regrets this situation and this decision, demonstrating a profound lack of respect on the part of West Ham towards the institution and the player."
West Ham did not address Lyon's comments about why the transfer had failed, but confirmed in an email to Reuters that the deal was not completed in time.
The club's manager David Moyes told reporters on Friday that the deal to take Benrahma to Lyon had "some problems with the paperwork at the last moment."
"But I only learned about it when I came off the pitch late last night," he said.
The deal was completed on Friday, with West Ham and Lyon both releasing statements confirming Benrahma's move.
Benrahma joins on a paid loan of £5.1 million ($6.4m) until the end of June with an option to buy him for £12.3m ($15.5m) and 10% of any future sell-on value.
Elsewhere, West Ham's sale of Pablo Fornals to Real Betis was also ratified on Friday after initial delays owing to technical issues.
Fornals' transfer was officially announced by West Ham on Friday, after Betis CEO Ramon Alarcon said the club were working to resolve the "computer error" issue that he said happened on the English club's end.
The Spain midfielder joined the LaLiga side on a permanent transfer after a four-and-a-half year spell at West Ham.
Sixth-placed West Ham visit Manchester United on Sunday.
Information from the Associated Press contributed to this report.