Akers, a 2020 second-round pick, is in the final season of his rookie contract with the Rams. He had 22 carries for 29 yards and a touchdown in Los Angeles' season-opening win.
Before the game Sunday, Akers sent a message on X saying, "I'm just as confused as everybody else. I'm blessed though."
McVay said Monday that Akers' social media post was "surprising."
"I feel very good about the clarity that was provided to him on Friday and Saturday, both through he and [agent] David Mulugheta," McVay said. "And that's unfortunate, but I feel like it was very clear in regards to our dialogue."
Last season, Akers spent nearly a month away from the Rams in the middle of the season after McVay said they explored the option of finding the running back "a fresh new start with another team." Earlier last year, McVay told reporters that he wanted to see more urgency from Akers. McVay said Sunday that this situation with Akers "is different" from what transpired last season.
Kyren Williams, who replaced Akers as the Rams' lead back, scored twice against the 49ers, rushing for 52 yards and a touchdown on 14 carries and catching six passes for 48 yards and a touchdown.