There are 3 achievements that are not story, but not missable: Open Sesame, Size Manipulator, and Precise Placement. You should earn all 3 of these by Chapter 2 at the latest.
That leaves 4 actually missable achievements:
Breakout – Go over the wall in Chapter 2, The Maquette. Use the key and prop it on the diagonal of the mini-Castle, then walk up the diagonal key in the normal-Castle and jump over the wall.
Crew Creatures – In Chapter 3, Gateways, near the very end, after you’ve used the Red Sphere to break down the very large wall/barrier, walk as a tiny person to the Green side, and go through a crack in the wall. Continue walking and enter the Dog House.
Into the Darkness – In Chapter 6, The Spiral, walk off an edge/commit suicide.
Run, Move, Run – In Chapter 7, The Exchange, the 2nd lever you pull will create a bunch of arches and require you to race across to a timed door on the other side. Make it into the timed door on your first pull of the lever. If you are worried about this, save right before pulling the lever and re-load your save if you fail.