Are there any moves that are more popular in databases of GM games but are objectively inferior? Usually in a particular opening position, if move A is more popular (in GM games) than move B, then either move A is objectively better than move B, or move A is equally good as move B. 

Are there any examples of moves that move A is more popular than move B in GM games but move B is objectively better?
It really depends on how broadly you want to define the openings. 

For example, while not popular at that level, GMs have played the Smith Morra. Of course, a standard open Sicilian is better.

The same goes for those, who have played the King's Gambit when trying for the Ruy Lopez is better.

The Ruy Lopez is probably objectively better than the Italian Game, but we saw the Italian played the last two days at times in the World Rapid and Blitz events.

The same goes for the Benoni, Benko, and Dutch. They are not horrible, but there is a reason the do not dominate high-level opening play. 

Anytime a GM needs to win, and plays a sharp opening that is not objectively best, and that happens a lot.

I am sure there are plenty of examples that are deeper into the opening, but this already shows how common it is.

Lastly, many GMs play sidelines, and have pet openings that are not considered best. They play them when they need an imbalance, and to win.