In the tutorial, it says, “Orientation doesn’t matter. The Vortex accepts shapes in any orientation, so you don’t need to rotate them before delivering them. I mean … have you tried rotating your camera?”
Also, in ‘Codex -> Research -> Shape Orientation’ it says, “The Vortex accepts any shape orientation, so there is no need to rotate the shapes beforehand. Why rotate the shape when you can just rotate the camera.”
PROBLEM ONE
That applies universally until trains. When loading trains, shape rotation matters. If you have a mix of rotations, non-matching rotations annihilate each other. This is unexpected. I realize a train wagon isn’t the Vortex, but the user cannot be blamed for thinking rotation simply doesn’t matter anywhere, and we should know about the annihilation mechanic.
So I suggest adding someting to ‘Codex -> Trains -> Shape Transport -> Shape Loaders’ about shape annihilation when packing wagons, highlighting that rotation matters here.
PROBLEM TWO
The Infinite Goals require exact rotation into the vortex. For instance, my first random goal was Su–Cu–, and the Vortex wouldn’t accept –Su–Cu until I rotated it. This contradicts the Codex. I can’t find anything in the Codex that explains this change.
So I suggest both adding a section somewhere in the Codex about Infinite Goals rotation requirements, and adding some doubt about the universality of the statements about the Vortex accepting shapes in any orientation in both the Codex and the Tutorial so it’s not contradictory when it happens.
Another option is to remove the rotation requirement for Infinite Goals, but it might be too late now.

the vortex and trade stations are the only structures that don’t care about shape rotation, it doesn’t apply universally, for example all the shape processing machines car about it, i.e. they produce different results if you input differently rotated shapes. as for the random operator shapes, it’s technically a bug that the orientation matters, but the game still tells you it’s the case when you hover over the randomized icon on the goal lines in the operator level screen