This is my first offering of feedback on the forums. I hope it's helpful.
The Indian children cried.
My first thought was, "Indian, or Native American?" I struggled with imagining both the children and the setting until the word "braids." And then I still was unsure of the setting, though I pictured some south-eastern Utah dry desert reservation.
Also, I think "cried" is an example of a "pushbutton word." From http://www.sfwa.org/writing/turkeycity.html - "Words used to evoke a cheap emotional response without engaging the intellect or the critical faculties." I would rather see why the children are crying rather than just being told that they are, because then I'll feel more for them.
Edwin Marks stepped away from repairing the fence to see the new arrivals.
How did they arrive? By bus? Train? Were they walking? Did they just appear out of nowhere? Who brought them? How many children are there? And if they're there unwillingly, how did the mysterious "school officials" get them there?
The girls shook with sobs from loneliness.
How does Edwin Marks know they're crying from loneliness? Can he read minds? And if not, is he reading their body language, and he can tell they're lonely, rather than scared, homesick, nauseous, etc.? If so, you might want to consider showing us that instead of just telling, especially if this is Edwin's POV.
The boys fought with tears running down their cheeks, refusing to let the school officials cut their braids.
The boys fought with tears, or with the school officials?
They shouted curses and wailed pleadings, each in their own tongue, none understanding another.
It was nothing new. In a few weeks most of the children watching their braids burning would be submissive to Pratt and the other administrators.
In a few weeks they would watch their braids burning? Or are the braids burning now? And if so, how? Are they being thrown on a bonfire? Are the Officials lighting them on fire individually? With matches? Flint and tinder? An acetylene torch? I'm confused as to what time period this takes place in.
A few would be dead.
By their own hands? By abuse? By supernatural forces? (Sorry, but these are the questions that popped into my head as I read.) 
Edwin spat, a private insult to Pratt he offered with every arrival.
Gertrude carried a bucket of water to Edwin. The school had let Gertrude keep her flowing black hair.
I'm guessing that the children have been renamed, hence the very non-indian names. But if this is true with Edwin, and the story is being told from his POV, and he is a former "new arrival," would he really think of himself as Edwin, especially if the new name was unwanted? Does he think of Gertrude as Gertrude because he doesn't know her real name?
I'm definitely curious about what is happening here, and why.