I don't see anything incorrect here. :nerd: Items that do not have an expand/contract indicator have a blank space where the indicator would be. This is standard for most/all UIs, eg (while certainly not the most stunning example of good UX) here is Windows:
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The .settings
folder has a blank space to the left, where its expand indicator would be if it had children. In your bottom pic which shows siblings, your yellow dotted line is in the wrong place. Your eyes should be looking at this line, in green:
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In other words, the icons are aligned horizontally for siblings, not the expand indicators.
Maybe you would like more indentation for children to better differentiate them from the parent? I will concede that the indentation amount is quite small, eg here it is highlighted in green:
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It is most common for the indentation of the child icons to align with the parent text, which would look like:
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Highlighted:
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Increasing the indentation would cause the tree to use more horizontal space, much more for deeply nested nodes. We purposefully minimized the indentation to reduce how often the tree needs to scroll horizontally.