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In Avengers: Age of Ultron, there is a scene in which Scarlet Witch manipulates the Avenger's to reveal their worst nightmares, but when it comes to mind controlling Hawkeye, he seems to be immune. This doesn't make sense to me as in the first Avengers movie, Loki had absolutely no problem controlling Hawkeye.
Is there any reason that I've missed that would indicate why Hawkeye become immune to mind control effects?
I think you misinterpreted the scene.
Hawkeye, being a very sharp archer, has shown to have heightened senses (refer to all his archery scenes through Avengers 1 & 2).
With such senses, he had heard Scarlet Witch walk up to him.
Basically he hit her before she had the chance to warp his mind. If you look at all the scenes involving Scarlet Witch manipulating the Avengers, she has specific hand gestures, and a flash of red. In case of Hawkeye, we do not see any such actions take place.
Hence, the conclusion:
Hawkeye is not immune to mind control. He merely neutralised Wanda before she had the chance to meddle with his mind.
It isn't explained exactly why Hawkeye didn't fall for Scarlet Witch's mind trickery, but we can find multiple possible in-universe reasons for it in the movie:
One possibility is, that it is because he was tricked and controlled by Loki earlier. The fact that his mind already had been tempered with before (and if we take it that Scarlet Witch's powers were created by Strucker using Loki's staff, then even by more or less the same power, the mind stone from the scepter) might have given him some kind of immunity towards it. Or it was the fact that he freed himself of the control (with the help of Natasha, though).
Another, maybe more likely, possibility could simply be that Scarlet Witch didn't even get as far as doing her mind tricks on him. As Stark07 suggests in his answer, too, Hawkeye might simply have been too fast and stopped her before she could even start her mind manipulation on him, as we know that he has particularly fast reflexes.
However, there is a deeper but rather out-of-universe reason why Hawkeye did not get affected by the mind trickery in relation to his role within the movie. In fact Hawkeye has to me always been the palest of all those MCU heroes, especially since he didn't have much to do in the 1st Avengers movie and never had much of a deep character, let alone so awesome powers as most of the other heroes. He always seemed to be quite an insignificant and powerless mere mortal.
But Age of Ultron went out of its way to give him more depth and significance. And not only that, the movie actually played exactly with those notions of supposedly being less significant and having less power than the others and turned those properties around into advantages. With this whole safe house angle and this secret family it provided Clint Barton with a grounding none of the others has. He is pretty much the only one of the Avengers having a working family and something very personal to fight for, as well as a chance for a life outside of all this hero mess. Yes, he might be less significant, he might have less power, he is just a human, but that is his strength. He is a voice of reason that does not have to worry about the whole world's fate all the time, since he has an actual non-Avengers life as an anchor. He can't carry the world on his shoulders, but he doesn't have to either. As put by Laura Barton herself:
Laura: You know I support your avenging, I couldn't be prouder. But I see those guys, those gods...
Clint: And you don't think they need me.
Laura: I think they do, which is a lot scarier. They're a mess.
Clint: Yeah, I guess they're my mess.
And I think this is what gave him the mental stability and groundedness to withstand Scarlet Witch's mind trickery, which was after all only playing with all the others' existing fears, dark histories and worries about the bigger picture. And while this might not be the exact in-universe reason Hawkeye could withstand the mind control, it is an important aspect of his character portrayal in the movie and the actual deeper reason for it. Saving all of them from the mental wrecks that Scarlet Witch turned them into at the end of the Wakanda scene was his character moment to finally play out his true strength and an introduction to the background of his character as substantiated further in the following safe-house scene.
Is there any reason that I've missed that would indicate why Hawkeye become immune to mind control effects?
He isn't immune as far as has been stated, he simply stopped her before she could do it. Compare this scene:
With the one before it:
Clint stops her before she can do that voodoo that she do. No hand waving, no magic red glowiness, hence no Mind Control took effect.
Notice earlier in the film, Maria Hill gives Cap a dossier on the Twins, including their power set. This would undoubtedly be shared with the team before heading into an encounter, a mission briefing. Just like they do with (soon to be) Klaw (Ulysses Klause). Standard operating procedure.
And then, as seen in the second clip above, Thor immediately lets the team over their radio/comm that Wanda ""tried"" to mess with his mind.
Further more, Clint's position at the top and end of the ship interior gave him a (pardon the pun) bird's eye view of the entire playing field. It's possible he saw the Thor being whammied, and Cap being knocked out and brain warped. The spot also had the benefit of only being accessible from one direction (short of flying). It was a carefully picked vantage point.
Clint was simply prepared for the possibility. Given that he is a high level spy/soldier/assassin for SHIELD, he has the skills necessary to prevent himself from being caught off guard from behind. Wanda on the other hand, did not have a history as a spy and does not have the skills to sneak around completely without notice.
Of course, it doesn't explain how she snuck up on Black Widow, who was not shown to be injured/knocked out like Cap, and she certainly isn't as Brawn over Brain like Thor. Bad writing.
Right before she shows up, a flash and alarm goes off on his bow. He has a proximity sensor on the bow. Right as she showed up, the flash happens on the bow and he stops her. Watch the scene closely.
Hawkeye is a highly trained super spy, and could probably hear Scarlet Witch sneaking up behind him. Black Widow also should have been able to hear Scarlet Witch sneaking up on her, however it is likely that Natasha was knocked out by some of the thugs she was fighting, and was either dazed or waking up when Scarlet Witch used her powers on her.
