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