Serge Gnabry seemed to have earned his side three points with a late goal, only for Freiburg's Lucas Holer to swoop in the 89th minute to the frustration of Kovac and his charges.
Muller saw much of the game on the sidelines, entering with 20 minutes to go - a decision that did not amuse wife Lisa.
"More than 70 minutes until he finally has a brain wave," she wrote on Instagram as her husband prepared to enter the action.
After the game, both Muller and Kovac attempted to play down the criticism.
"It was out of emotion. In retrospect I don't think it was super. But she just loves me, what should I do?" the Germany star signalled to Sky.
Kovac added: "There's nothing to clarify. Obviously it wasn't Thomas himself who wrote that."
Bayern currently lie second in the Bundesliga, four points behind leaders Borussia Dortmund.
The two pace-setters clash in the next round of league fixtures on November 11, when Bayern visit Signal Iduna Park for the first Klassiker of the season.