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In the Military, there are three units, each with its own patch: Scouting Legion, Military Police and Stationary Guard.
Unit's Patches
Left to Right: Scouting Legion, Military Police and Stationary Guard

So far in the anime (up to episode 12), from these three we've seen (if I didn't miss any) only the Stationary Guard's patch.
Stationary Guard patch

Most of the main characters (Eren Jaeger, Mikasa Ackerman, Armin Arlert, Jean Kirschtein and others) are in the Scouting Legion. However, they seem to have a different patch that exhibits two crossed swords. They've been wearing this patch since (in episode 2) formation, and the people in charge of training then were also wearing this patch.

Crossed Swords patch Crossed Swords patch, seen in formation

Even characters, such as Annie Leonhardt, that belong to the Military Police exhibit the Crossed Swords patch.
Annie Leonhardt with the Crossed Swrods patch

What differs in the anime from the manga?
Were both the patches and the character's military affiliations changed?

  • 1
    The crossed swords over a shield emblem is the "Training Corps", not sure why the image of Annie has that emblem, maybe it was a flashback picture from when she was part of the training corps? – Jon Lin Jun 23 '13 at 20:40
  • @JonLin But the picture where Annie, Reiner and Bertholdt appear, with Mikasa's back facing us is on episode 8 (I think). By then they're fighting Titans in Trost (around the time Eren was eaten by the bearded Titan). – JNat Jun 23 '13 at 21:13
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After watching episode 13, I realize I misunderstood some things.

So far in the anime (up to episode 12), from these three we've seen (if I didn't miss any) only the Stationary Guard's patch.

This is most likely wrong, as we'd seen Levi before, and he belongs to the Scouting Legion. See this image from episode 13:
Levi and the Scouting Legion's patch

In episode 13, we also see the Military Police's patch, although from a distance:
Guards standing, with the Military Police patch
The patch is visible on the arms of the guards standing by the cell

This means we've seen all three patches (Scouting Legion, Military Police and Stationary Guard), plus the Crossed-Swords patch.

Now, my misunderstanding came from the fact that the characters I mentioned in the question are listed in the Shingeki no Kyojin Wiki as affiliated either with the Scouting Legion (Eren Jaeger, Mikasa Ackerman, Armin Arlert and Jean Kirschtein) or the Military Police (Annie Leonhardt).
However, episode 13 also shed some light on this matter, when Jean identified Marco Bodt as "The 104th Training Corps Leader of Squad 19, Marco Bodt."
Marco Bodt's corpse

Also on episode 13, Levi tells Eren he'll accept his application to the Scouting Legion:
Levi telling Eren he'll accept him in the Scouting Legion
NOTE: The Scouting Legion is dubbed/subbed as Recon Corps in the anime

This would mean that the characters mentioned in the question still belonged to the Training Corps, and that the affiliation mentioned in their SnK Wiki pages (which, in addition to the fact that I was under the impression they had already "graduated" from the Training Corps, caused my misunderstanding) is, presumably, from the manga, which is ahead in the plot.

Basically, as JonLin wrote in the comment below the question, the Crossed-Swords patch belongs to the Training Corps, and no affiliation seems to have been changed.

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