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I was able to reproduce this non-issue with the following steps:
1. Create a new Sigil epub2 book.
2. Enter Chapter 1 in Code View mode, highlight it and apply a heading tag, e.g. h1
3. Repeat step 2 for Chapter 2.
4. Generate an NCX TOC to add an id value to the Chapter 2 h1 tag.
5. Switch to Book View mode, select Chapter 2 and copy it.
6. Paste the text and select No, when asked whether the text should be pasted as plain text.
7. Select the text pasted in step #6 and click the p button on the toolbar. This will change the tag from h1 to p, but won't delete the id value.
(Of course, you could also copy the heading tag in Code View mode, select only the copied text and click the p button.)
IMHO, this is pretty much the only way how the OP could have ended up with duplicate ids.
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