Strangely, yes. While not all fighting-types do this, many consider flexing to be a form of communication. Think of it as similar to the way two growlithe sniff at each other’s tails when they first meet. Just as this is a way for growlithe to understand each other, two fighting-types display for each other to show off their power, which in turn allows them to understand a number of things about one another, including how they train and so forth.
It should be noted that when I say that fighting-types compare how they train with one another, I don’t mean that they try to establish dominance. Rather, it’s a form of camaraderie, an act in which two pokémon engage in friendly appraisal. This is especially common with pokémon on the same team, as fighting-types will gauge each other’s progress for the sake of helping one another to develop their talents.
So in short, it’s nothing to worry about, @samthewindwaker. It just means that your pokémon have been putting forth a particular amount of effort in their training regimens lately, and they’re discussing their progress.
(Assuming, of course, that they aren’t literally fighting one another or displaying any form of explicit aggression towards each other.)
The Pokédex According to Bill 