There was definitely an issue with the Insert Files utility in Sigil v1.0.0. I can see the commit where it was fixed, but I can't find any conversations about how the issue manifested.
If you're using v1.0.0, I'm betting this was the same issue. If so, the good news is it's been fixed, but the bad news is that a new version with the fix hasn't been released yet. We're hoping soon(ish).
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