So, I'm a few hours into the game and I'm pretty much enjoying it so far. There's a few hiccups with the mouse control that I'm kinda not liking, but I guess I can live with that, but something just happened that kinda ground my gears a little.
For a game that's pretty much done everything else fairly well so far, this is... kinda a moment of FAIL.
So, I'm stuck in a room and I'm trying to figure my way out. A few seconds of searching and I realize that there's a tall wooden box inside the room that I can push around. "Ok," I says to myself, "I'm sure this is critical to me getting out of here." So I start shoving the box around. And push it up against a wall.
And then realize that I was supposed to use the box as a ledge to get up to a grate on the opposite side of the room. I could then kick in that grate and proceed. Except now the box is up against the wall, and I can't get on the other side of it to push it. Nor can I pull it. Nor has there been a save terminal within the last 20 or so minutes of play time.
Designers: Good game. Really, I've been enjoying it. But this moment right here? FAIL.
Yes, I know I should have looked more carefully before I started pushing that box, but really? How hard to put in a pull function? How hard? Or, at the very least, design the room such that you can't get a box stuck in such a way that you can't push it out to where you'll eventually need to get it to?
Now I've got to reload my last save and replay a pretty large section of the game, because of something as mundane as this? Boo. Very much boo.

I think for the most part, the box pushing puzzles are designed to be impossible to screw up.
Which one did you manage to break?

I just took some snapshots of the display on the X-Ray machine showing that the baddies have people stuffed in those crates. Went back only to find that Pey'j had gotten himself caught. They're dragging him off to the loading dock, and I've got to go after him. I end up in the room I left him in. There's a big box, a big door with a slit in it, and nowhere to go except the grate leading to the passage I just came from, and another grate leading to another passage. (Where I assume I need to go, but I didn't see that grate at first.) So I pushed the box toward the door, at first, thinking I needed to climb up and do something with the slit in the door. But once I got the box next to the door, I couldn't move it away from the door afterwards, and the last save terminal was down at the bottom in the elevator room I'd used to get up to this place to begin with.
That was like fifteen - twenty minutes of solid play before. So, I was a bit irked.

I'm assuming you haven't got back to that bit? You were doing it right the first time, I don't think the game allows you to mess those boxes up. You are meant to push the box up to the door and then go into camera mode and use the right click to fire one of those wrist discs at the door control button on the other side of the door to open the door. If a box does somehow get stuck you can always exit that section and when you come back the box will be reset.

You were actually right the first time. You fire your disc launcher through the slit to hit a switch that opens the door.

Yep. Thanks, gang. I stumbled around for a few more minutes before I caught on to that idea. Guess I didn't break the puzzle after all. Hooray! Heh.