The dispute stems from LaLiga's refusal to register Gavi's new Barca contract because the Catalan club are deemed to be in excess of their spending limit beyond the end of the season.
However, a court ruling on Tuesday, as first reported by ESPN earlier this month, said Barca missed the subsequent deadline to officially file their lawsuit.
Sources at the club said they did not send the paperwork late and confirmed they planned to appeal the decision and continue their fight to register Gavi's deal.
Gavi, 18, signed a new contract at Spotify Camp Nou last September until 2026. LaLiga say they will not register the multi-year deal because Barca need to cut as much as €200 million from their outgoings ahead of next season.
Barca's annual spending limit -- which LaLiga impose on all clubs as part of their financial fair play rules -- stands at over €600m. It is greatly inflated, though, by the sale of club assets last summer and is expected to be reduced later this year.
In the worst-case scenario, Gavi could technically become a free agent at the end of the campaign if there is not a resolution before then, although sources at Barca have told ESPN they do not expect that to happen.
Despite losing his first-team registration, he will still be able to play for Barca in what remains of the season under his previous enrolment as a youth-team player.
Gavi has been an ever-present for Barca since breaking into the team in 2021. He has already made 84 appearances for the club, helping him win the prestigious Golden Boy award last October ahead of Jude Bellingham.