When I create a new Theme Section and use a self closing tag e.g. "<a ... />" at the beginning of the section, the self closing tag is duplicated in multiple places in the section. The tag is also repeated into the following footer section.
In the Theme Editor, if I put the section at the beginning of all sections and after I save, the editor will re-arrange it and put the section as the last section.
In the image, you can see "repeatingxxx" seven times.
Next image is from the browser console.
I am attaching both versions of the Theme Sections and the HTML source code. I just downloaded the Boundless Theme this week.
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That <a>...</a> inside <ul> above the <li> doesn't look good. The only element allowed inside an <ul> is <li>. So the HTML as seen here on the screenshot with the page source is invalid and might impact the whole layout of the page. Not necessarily the root cause, but thought I'd highlight that.
It's not a Shopify problem, it's broken HTML and browser error-recovery.
The .html in your ZIP does not show any repeats -- try looking at "View Page source" for unprocessed code and not in "Elements", where browser (unsuccessfully) tries to fix the HTML structure.
Now the question is why do you think self-closing <a> is valid?
It's not a void element, so it can't be self-closing, most probably browser treats it as opening tag and have problems since there is no closing tag.
Try any valid void tag, lake <br /> (or any of area, base, br, col, embed, hr, img, input, link, meta, param, source, track, wbr).