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Steve Rogers and Howard Stark seem a little... too close to each other, moreso Stark towards Rogers. Just look at how Stark looks at Rogers before the injection! More than a few fans have wonder who he was jealous of with Howard and Peggy "fondueing".
When Steve asks the Howling Commandos to go back to the front with him, two of them, Jones and Dernier, converse in French and they're sitting awfully close to each other. Makes you wonder what else they use that for...
A lot of the lines between Stark and Banner sound kinda flirty, and a thousand fanfics were launched in the single moment when Stark randomly pokes Banner in the stomach and Banner just puts up a mild, vaguely amused, "Oh, you" type of protest note On the gag reel, RDJ pinched Mark Ruffalo's butt instead; hilariously, it didn't require them to play the scene all that differently. Couple that with the scene where the Hulk saves Iron Man twice in rapid succession, and the fact that these two are the only two members of the Avengers to hit it off the instant they meet...
Stark: Finally! Someone who speaks English.
They are seen driving off into the sunset together at the end of the movie.
It's toned down in the movie proper, but the featurette included on the DVD shows that Tony is a little... excited about the Hulk.
Perhaps it's less suspect in Asgard, but the way Thor cupped Loki's cheek and neck while asking him to come home seemed a bit affectionate(in a not so brotherly manner) to mortal audiences.
Their lips were mere inches away◊ from each other when Thor pulled Loki out of his seat on the jet.
Cap and Thor; that searching look Thor gives Cap when Cap goes on fighting after he's hit...it's like a light went on inside his head. Fan fiction appeared for these two months before the movie was released, but that moment helped make it less of a niche pairing.
Fitz pats Ward in uncomfortable ways a few times, including what looks like a broslap on the backside, and seems to idolise him more than a little. He also responds to Ward's betrayal with a similar amount of distress to Skye, who was Ward's Love Interest.
Simmons and Skye develop something of a Romantic Two-Girl Friendship over the course of Season 1. In particular, Simmons' response to Skye's life-threatening injuries is to spend the best part of an episode stroking her forehead and hair. Then there's the fact that they've hugged at least as many times on-screen as they have with their canonical love interests...
Following Ward's betrayal and Simmons' temporary departure, Fitz develops a relationship with Mack that is reminiscent of his relationship with Simmons in Season 1. A lot of Fitz/Ward shippers have defected to Fitz/Mack for this reason. It's even been noted that in Season 2 the Mack/Fitz/Simmons dynamic operates almost identically to the Fitz/Simmons/Triplett Love Triangle in Season 1.
Simmons has a rather transparent girl-crush on Bobbi Morse, a.k.a. Mockingbird. Bobbi herself has more of a Cool Big Sister attitude to Simmons.
When Fitz sadly tells Mack and Hunter how badly his attempt to confess his feelings for Simmons went and how he's sure she doesn't feel the same way to the point of leaving, Hunter is quick to assure him that "it's her loss". It's a sweet moment, but it does come across as a little flirtatious at the same time.
At the end of the movie, Sam watches Steve sleep while Marvin Gaye plays.
Several reviewers have noted that Sam plays a role normally filled by the Love Interest in a superhero film (emotionally balanced, nurturing person who gets the hero to open up emotionally in a supportive way). They even have a Meet Cute, for goodness sake.
As per usual for a Captain America film, there's Bucky and Steve's friendship. Bucky becoming the Winter Soldier does not diminish the vibes; if anything, it increases them. The amount of Steve/Bucky Fan Fictionskyrocketed when this movie came out, no thanks to this:
When Natasha is trying to set Steve up with someone, he complains that "it's kind of hard to find someone with similar life experiences." Yeah, Steve, who could you find that grew up in 1920s/30s Brooklyn, fought HYDRA in World War II, was made into a Super Soldier, and was frozen and thawed in the 21st century? Who could possibly fit that description?
"I knew him." Yes, Bucky, yes you did. The Helicarrier battle between them just makes it worse, with Steve literally begging Bucky not to make him do this. Then when Steve no longer has to fight with the lives of over twenty million people on the line, he drops his shield into the water and refuses to continue their fight, getting the crap beaten out of him in the process, and falls into the Potomac below towards near certain death. Who saves him? Bucky.
After the movie got its Honest Trailer, Groot and Rocket became an obvious copy of Science Bros.
Also when the team is incarcerated together in the Kyln and a large inmate gets a little too touchy-feely with Quill, Groot and Rocket step in to protect him with Rocket explicitly stating that he was their "booty." note Rocket and Groot wanted to collect on the 40,000 unit bounty placed on Quill's head.
Yondu and his First Mate Kraglin. The two are rarely seen apart, and Kraglin is evidently privy to a lot of Yondu's secrets and quirks. Yondu and Kraglin even seem to act like surrogate parents for Peter Quill, with Kraglin remarking that Quill "turned out okay" and Yondu beaming proudly when he finds out Quill literally Trolled him.
Gamora and Nebula are typically trying to kill each other during their few scenes together, but one deleted scene has them more literally at each other's throats. The scene is titled "Sisterly Love". That's not what most are thinking.