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"I don't have a spell for everything, Rarity," Twilight said exasperatedly - 'exasperatedly' reads awkwardly to me; I would suggest putting a comma after 'said' and using 'exasperated'
As the sounds of battle cries reached his ears, Soarin looked over his shoulder as they galloped; - two uses of 'as' fairly close together, not a big deal, but you might consider tweaking it
The girls all had their eyes closed and seemed to concentrating just as hard as Twilight. *The girls were atop a nearby hill and Soarin and Doctor Whooves were sitting at its base, resting and waiting for something to happen. - same repetition issue, but this time with 'girls'
I admit, this one is a bit of a toughie. *I'm used to having a bit more in the way of equipment, or an enemy with an obvious weakness. - also repetition, this time with 'bit'
Tirek peered at the girls andd seemed to reach the same conclusion - too many d's in 'and'
With an ease borne of long experience brought it down on Tirek's head with a mighty crack. - I think you're missing a 'he' in this sentence
"Yeah, you've got me pegged. *You can do whatever you like, I'm going to surrender." - I assume you're missing a 'not' in the sentence about surrender
But focus. *You get over there so you can see the girls; they ought to be getting their spells done soon, unless the Twilight Sparkle messed up the spell, in which case it's been nice knowing you. - not sure about that 'the' in front of 'Twilight Sparkle'
he clenched his fist tightly and redoubled his rage filled-trembling - this would read easier for me if you moved the dash so it was between 'rage' and 'filled'
Applejack shoved him back down on the bed as fast as she could mange and . - seems to be something missing/added before the period
As was her way, the tan mare looked upon them dispassionately - 'upon' reads oddly to me, consider a different preposition
N-no, Private." *He cleared his throat to buy for time - I think the 'for' is out of place here
"So, how long was I out? *I know these things aren't easy to set up." - this is a context question: I assume he means a medical tent when he says 'these things', but I found it confusing as I was reading
Highly checked her wristwatch. - need to change to 'Highfly'
Applejack frowned. *"Didn't seem proper to mention it, long ah thought you might be hurt. - I think there's a word missing after 'long'
It was funny... not that Soarin was going to laugh at the Scorpan. - take out 'the' before 'Scorpan'
Scorpan shook his head bemusedly. *"What do you think you're going to do about it?"
*********** Highfly frowned thoughtfully. *"Well, I do have some tranquilizers..."
*********** Scorpan shook his head bemusedly. - Repetition of 'bemusedly'
He'd seen how hard the human could punch. - This seems to break the convention of using 'hyu-man', not sure if it's intentional or if it happens other places
Highfly sounded slightly annoyed. *This was a rare occurence. - I think this might read better with a semicolon instead of a period and changing 'This' to 'that'
It's getting late; I'm going to have to call an end to visitors hours." - I believe 'visitors' should be possessive
"Wing Sergeant, you march over to Ponyville *as soon as possible and don't you leave until one day from tomorrow. - I think you mean 'week' instead of 'day'
That's all I got. You might want to skim for other places where you might have shifted between 'human' and 'hyu-man' if you want to stay consistent, but that's about it.