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Ousmane Dembele scored late on in the second half to seal all three points for Barcelona at the Camp Nou on Monday.
However, Messi was far from happy with the referee's performance and expressed his dissatisfaction at half-time.
According to Spanish newspaper Diario AS, the 33-year-old Argentine superstar boldly claimed that Latre 'wants to give me a card... incredible.'
Messi's claims appear to suggest it was a deliberate attempt to see him suspended for Barcelona's important El Clasico clash with Real Madrid on the weekend.
The six-time Ballon d'Or winner will be eligible for Barcelona boss Ronald Koeman to select after avoiding a fifth league caution this season.
Barcelona's crucial victory over Valladolid keeps them in the La Liga title race.
The Spanish side are second in La Liga and are one point behind league leaders Atletico Madrid.
Los Blancos, meanwhile, are two points behind Barcelona and three points adrift from Atletico.
Speaking ahead of the Valladolid match, Koeman insisted that he wants Messi to remain at the Camp Nou amid uncertainty surrounding his future.
The 58-year-old Dutchman said: "Of course it's a very important matter [Messi's future].
"We're trying to do our best so that Leo stays. But that moment [of his announcement] isn't going to be next year."
Messi, who endured a high-profile public spat with Barcelona last summer, will see his current deal expire in the summer.