For some reason, when I click a button, be it in the customize buffer or hyperlinks in org documents, it sometimes works, and other times the whole buffer shifts to the left like a single pixel and it sets a mark (it says so in the minibuffer). The button is not clicked in those instances.

Has someone experienced something similar? Is there a way to improve this?

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as you said, display-line-numbers do the shift when the cursor change the quantity of numbers in the line, from 9 to 10, for example, maybe if you use `absolute` can help, or you use can try change a fixed width from the line number, so it cannot change the window size.

Also, you can see this example from modus-theme to help you.

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