Your first example (Nero's ear) was a visual continuity error, not a plot hole.
The thinner atmosphere of Vulcan was first mentioned in 'Amok Time', way back in TOS. It's reasonable to conjecture that upper atmosphere would be thinner. That's just bad science, though - I wouldn't call it a 'plot hole', otherwise we'd have to toss out half of Trek. It should be categorized under a different subset of 'movie mistakes'. Mistakes like that don't necessarily subtract from a film unless they're very glaring mistakes.
What STXI suffers from are not plot holes, per se, but plot contrivances and coincidences that really strain credulity. It's not a plot hole that Spock uncharacteristically marooned Kirk on an ice planet a few hundred yards where Spock Prime was hanging out with wooden (!) torches - a few kilometers from Scotty, no less - but it is fairly ridiculous and makes the Star Trek universe look about as large and populated as the North Mariana Islands. Only smaller.
Though a plot contrivance could be described as a sort of shallow plot hole. Not one that breaks your axle, but it sure roughens up the ride.
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Then there are things which could be considered 'shallow' plot holes because they aren't explained onscreen. For example, how did Vulcan send a distress signal if the drill jammed all communications? And if they were able to send out a signal, why not mention 'oh yeah, and there's a huge warship in orbit'? Why were there no defenses on Vulcan or Earth? All it took to disable the drill were hand phasers. Are we really supposed to believe that there aren't aircraft or armed shuttles that could blast the thing, or even weapons that could be fired from the ground?
Nero's motivations certainly qualify. 25 years of hatred for the man who tried to save his planet... okay, if he's a madman, I could maybe buy that. But I feel at some point one of his crew would get fed up with the obsession, realize the ramifications of destroying entire worlds, or be worried about mucking up his own timeline that he'd put a distruptor up to the back of Nero's head and pull the trigger.
There could be explanations for these things, but they didn't bother to give us any. They certainly are plot implausibilities, so I categorize them as 'shallow plot holes'.
Oh, and concerning the cut line about the timeline 'trying to mend itself' above - I guess that rules out the alternate reality/parallel timeline, doesn't it?