This looks like fixed-pattern sensor noise rather than a Photoshop stacking problem. Some sensors, including certain Canon models, can show a repeating grid or banding pattern when very dark areas are pushed hard in post. Stacking reduces random noise well, but it does not remove noise that is fixed in the same place from frame to frame, so the pattern can remain or become more obvious.

Why it happens:

• It is related to the camera sensor/readout pattern.
• It tends to show up more when shadows are heavily lifted or an image was underexposed and corrected later.
• Different camera models and sensor generations vary in how visible this is.

How to reduce it:

• Expose more generously in-camera so you do not need to push shadows as much later.
• Avoid strong recovery of severely underexposed files.
• If possible, lower contrast/shadow boosts in the affected areas.
• In general, using a camera/sensor with better low-light pattern-noise performance helps.

So the repeating squares are most likely sensor pattern noise being revealed by shadow boosting; stacking can’t fully cancel that kind of noise.