I’m having a couple of minor, but annoying, compatibility issues that are, I think, similar in nature.
1) Amazon affiliate links always throw up errors, even if they’re good. I don’t know what the solution is here — it might just be to have the plugin skip them. (Although it would be helpful to have it note that it skipped Amazon links, so the user knows to look for them to check them manually.)
2) One of the sites I have this installed on also uses a footnote plugin that works by wrapping the footnote text in shortcodes. (Basically, it looks a bit like wrapping a link with HTML code when writing a webpage, but using shortcode syntax.) A lot of my links are in these footnotes, and the brackets seem to be confusing your plugin, so it’s not recognizing where a URL begins and ends. The footnote plugin is called Easy Footnotes.
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