For one thing, all of Pratt's character's responses are barbed with oddly sexual undertones. Imagine if you worked with one of your exes. Making those kinds of comments would lead to a sexual harassment suit.
Mostly though its just a matter of cliched, limiting, character types.
Let's not get carried away. He made two sexual jokes. TWO. That's it. Most of his dialogue had nothing to do with sex. Second, it's obvious they know each other and are comfortable with each other. She doesn't seem hurt or perved out by his comments because GASP! she seems like a grounded female character! Sexual harassment? Maybe, but obviously it's not because she seems to be able to take a joke.
I could see the point in Whedon's obvious low blow if Owen and Claire didn't know each other and he was just being piggish to be piggish because "Rawr Imma MAN!" But that's not the case.
And really, Malcolms behavior in the first film seems much more in bad form than Owens. Why? Well, he didn't know Sattler beforehand. He just meets her and starts commenting on her looks in front of her colleague/partner as well as other strangers. He also totally touches her a lot during his Chaos Theory demonstration AND questions Grant about her availability. Yea, Ellie takes it in stride. But SO DOES CLAIRE! We don't know the entire context of Owens and Claires relationship, but from what we do know his PG-13 sexual jokes are fine with her.
Why no outrage over Malcolm? Yea, his suggestive nature is tamer than Owens more upfront jokes...but why does that make it better? It doesn't. It's much more lecherous imo because Malcolm makes his position known to her and the rest of the group from the get go. That is sexual harassment too, if you want to go there. So why not call this out? Nostalgia? Bias? Or has PC crap just taken over everything so completely?
I will concede the character types are cliched, but so what? Again, we don't know the whole context. If anything that clip semi confirms what I hoped the film would do: Give the characters some down to Earth qualities.