The "filler" folks are talking about isn't the sort of filler you'd see in, say DBZ or Bleach. AoT's filler comes in the form of long, drawn-out sequences and narrative blocks that take so long to reach their point that much of the material becomes redundant.
A couple of examples: (SPOILERS FOR AOT ARCS ONE AND TWO FOLLOW)
1.) The constant, absolutely unnecessary reminder that Eren is intent on killing "every last one" of the Titans. We get this message pretty clearly when he initially signs up for military training, again when he's in the barracks growling into his bowl of soup, again when he's telling Arman to get off his back, again when he's telling Mikasa to stop hovering over him like a mother hen, again when he's trying to justify his actions to Levi...
Surely you see where this is going. Plots don't move forward when characters repeat themes and statements ad infinitum; a little repetition is sometimes necessary to remind the audience of what's going on in a long, complicated arc, but the action in the Trost arc is very much limited to, "Titans show up, eat Eren's mother, wreck a bunch of shit, and Eren's mad."
That's all that's accomplished in those thirteen episodes—and that's a lot of damned screen time for so little to be done.
2.) Every encounter with the Titan-Shifters.
It should've been bang-on obvious to the audience who the Female Titan was from the first time she showed up, and yet it takes the better part of nine episodes for the cast to catch on. Foreshadowing and tipping one's hand to the audience before the cast are normal tricks in narrative development, but the ignorance of the main cast borders on the absurd—particularly in light of Eren's ability to Titan-shift.
The Scout Regiment has to capture the Female Titan not once (in the forest), not twice (inside the walls), but three times (after Eren throws Mikasa up the wall after the Titan)—and even then, what we're left with is the Female Titan's human form (not posting the name just in case someone's missed her identity) enclosed in a crystal, and once again, we've gone thirteen episodes and all we've managed to do is deal with one Titan.
Nothing else of any consequence has happened in the course of those thirteen episodes. We have some slightly better understanding of how Eren's Titan-shifting ability works, and we know he's not the only one—but apart from that, Mikasa's still denying she's in love with him, Eren's still being a shit to Mikasa at every opportunity, Arman's still a whiny goofball who somehow manages to pull victory out of his ass at the last second, and Jean's desperately trying to get into Mikasa's pants whilst hating Eren.
Sure, more people are dead, but in AoT, named characters function as, "Look, someone with a name and a backstory got munched on—DRAMATIC!" The core cast is still pretty much untouchable at this point; no matter how dire their situation is made to appear, Eren, Mikasa, Arman, Levi, et. al. are in no danger of being offed anytime soon, because the story revolves around them—so everyone who gets stomped, eaten, or thrown bolo-style by means of their mobility gear is really just a footnote in a story already crammed with them.
...again, I say all this as someone who owns the currently available episodes of the series, and who's found a way to enjoy the anime in spite of its hackneyed writing—but seriously, man, you can't tell me the thing's not got more padding than a psych-ward cell. Eesh.