It just means you're obviously setting up characters to make another character look good. But you're not necessarily always doing that.
I think that depends on how it is done. Setting up characters to be deliberate foils for one another, intentionally using one character (and their methods) to demonstrate why another character may be wrong, is a perfectly legitimate technique in fiction (more so in some genres than others). It only becomes a problem when the second character is being written in a way that is contrary to their previously established character, and I wouldn't call the first character a Mary Sue because of it. If we're going to get really technical that's something I like to refer to as 'shitty writing.'
I think it's even worse in comics than most, take for example the fact the title character is GENERALLY going to come off looking better when it comes to conflicts with guest stars in his or her own book, even when the guest star could legitimately give the title hero a hard time under 'normal' circumstances. That sort of thing doesn't, imho, make anyone a a Sue. It's just...predictable.
I do get what you're saying, maybe they are Sueish 'moments.' I'm probably just a little ticked because a lot of the characters I like are (fairly or not) accused of being Sues, and I prefer to assume that I'm right and everyone else is wrong rather than accept I buy into hype and Sueish displays of forced awesomeness.