According to L'Equipe, the Chilean stormed off the field after being asked to remove his bib.
It is believed that the bibs indicated who would be starting tonight's Coupe de la Ligue clash with Bordeaux.
However, Girard played down rumours of unrest in his pre-match press conference.
"He had headaches, he went to look for aspirin," said the 58-year-old. "The group is good. There are bad moods sometimes but that's the life of a group."
Estrada joined La Pallaide from Universidad de Chile in 2010.