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There's a QR code in 16-cubes city but it has been blocked by some obstacle.
And I tried to fix the picture to make it clearer but there's still something missing in the top left part.
You can clean that up further and replace the missing parts that are unfinished but known:
But it still doesn't scan.
Does anyone have any ideas about this?
There is one room in particular that provides what you're looking for. You don't need to copy NPC dialog, though part of the fun is copying the other wall-writings for later consideration. So there is no single intended method (I imagine most people will look online)—your method could work, though it sounds frustrating.
Want a hint for that room's location?
It's off of the waterfall room.
Want an even bigger hint?
A pillar in the room links the code to an English pangram (sentence containing every letter of the alphabet).
And to give it away:
In the tree room above the waterfall, a fox jumps over a dog next to this pillar, which reads all the way around: "The quick brown fox jumps over the lazy dog." (image)
Controller inputs are only associated with tetrominos once.
Where?
Towards the top of the map, in the tree near the octopus building that houses the solar system model.
What's inside?
A puzzle that displays tetromino blocks based off of controller inputs, and an anticube prize for cracking the nearby pillar's code. (image) (link to finished cipher)
The classroom in the 8-cube Blade Runner city then shows how to interpret the pillars with tetromino inscriptions. Here's one wall, but relate it to the others:
Like the alphabet, there isn't one proper way to do this, but you might be interested in the 16-cube temple's classroom. Instead of trekking back, this is what it looks like:
Hint:
Those are "equals" signs, and the last picture is arithmetic. Also, the figure/ground is confusing—pay attention to the box and its internal vertical/horizontal lines, not the "C" shapes. (link to finished cipher)
Best Answer
The 16-cube area is the ancient version of the temple/science warp zone. That QR code was under construction long ago, but it now appears "fully realized" on the same wall in the temple/science warp zone. So it can be completed—indeed, it has been.
If you're curious, the QR code links to...
This is a higher resolution of the screenshot, from the PC gersion of the game:
I have then extracted the QR code, converted it to black and white, removed Gomez and some dust, and applied a median filter. This is the complete QR code, which you can scan on a website.