[Doitsu]

I was able to reproduce this issue with a commercial epub2 book (Crichton, Michael - Dragon Teeth, Harper Collins, 2017). I simply opened the book and selected Tools > Index > Create Index.

The original order of the first 4 XHTML files in the Book Browser was:

cover.html
title.html
copyright.html
contents.html

original spine

Spoiler:

  <spine toc="ncx">
    <itemref idref="my-html-cover" linear="yes"/>
    <itemref idref="title"/>
    <itemref idref="copyright"/>
    <itemref idref="toc"/>
    <itemref idref="map"/>
    <itemref idref="introduction"/>
    <itemref idref="part001"/>
    <itemref idref="chapter001"/>
    <itemref idref="chapter002"/>
    <itemref idref="chapter003"/>
    <itemref idref="chapter004"/>
    <itemref idref="chapter005"/>
    <itemref idref="chapter006"/>
    <itemref idref="chapter007"/>
    <itemref idref="chapter008"/>
    <itemref idref="chapter009"/>
    <itemref idref="chapter010"/>
    <itemref idref="chapter011"/>
    <itemref idref="chapter012"/>
    <itemref idref="chapter013"/>
    <itemref idref="part002"/>
    <itemref idref="chapter014"/>
    <itemref idref="chapter015"/>
    <itemref idref="chapter016"/>
    <itemref idref="chapter017"/>
    <itemref idref="chapter018"/>
    <itemref idref="chapter019"/>
    <itemref idref="chapter020"/>
    <itemref idref="chapter021"/>
    <itemref idref="chapter022"/>
    <itemref idref="chapter023"/>
    <itemref idref="chapter024"/>
    <itemref idref="chapter025"/>
    <itemref idref="chapter026"/>
    <itemref idref="part003"/>
    <itemref idref="chapter027"/>
    <itemref idref="chapter028"/>
    <itemref idref="chapter029"/>
    <itemref idref="chapter030"/>
    <itemref idref="chapter031"/>
    <itemref idref="chapter032"/>
    <itemref idref="chapter033"/>
    <itemref idref="chapter034"/>
    <itemref idref="chapter035"/>
    <itemref idref="chapter036"/>
    <itemref idref="chapter037"/>
    <itemref idref="chapter038"/>
    <itemref idref="chapter039"/>
    <itemref idref="chapter040"/>
    <itemref idref="chapter041"/>
    <itemref idref="chapter042"/>
    <itemref idref="chapter043"/>
    <itemref idref="chapter044"/>
    <itemref idref="chapter045"/>
    <itemref idref="postscript"/>
    <itemref idref="note"/>
    <itemref idref="afterword"/>
    <itemref idref="bibliography"/>
    <itemref idref="footnote"/>
    <itemref idref="bm001"/>
    <itemref idref="bm002"/>
    <itemref idref="bm003"/>
    <itemref idref="abouttheauthor"/>
    <itemref idref="alsoby"/>
    <itemref idref="aboutpublisher"/>
  </spine>

after selecting Create Index the Book Browser order was changed to:

contents.html
cover.html
title.html
copyright.html

updated spine

Spoiler:

  <spine toc="ncx">
    <itemref idref="title"/>
    <itemref idref="copyright"/>
    <itemref idref="map"/>
    <itemref idref="introduction"/>
    <itemref idref="part001"/>
    <itemref idref="chapter001"/>
    <itemref idref="chapter002"/>
    <itemref idref="chapter003"/>
    <itemref idref="chapter004"/>
    <itemref idref="chapter005"/>
    <itemref idref="chapter006"/>
    <itemref idref="chapter007"/>
    <itemref idref="chapter008"/>
    <itemref idref="chapter009"/>
    <itemref idref="chapter010"/>
    <itemref idref="chapter011"/>
    <itemref idref="chapter012"/>
    <itemref idref="chapter013"/>
    <itemref idref="part002"/>
    <itemref idref="chapter014"/>
    <itemref idref="chapter015"/>
    <itemref idref="chapter016"/>
    <itemref idref="chapter017"/>
    <itemref idref="chapter018"/>
    <itemref idref="chapter019"/>
    <itemref idref="chapter020"/>
    <itemref idref="chapter021"/>
    <itemref idref="chapter022"/>
    <itemref idref="chapter023"/>
    <itemref idref="chapter024"/>
    <itemref idref="chapter025"/>
    <itemref idref="chapter026"/>
    <itemref idref="part003"/>
    <itemref idref="chapter027"/>
    <itemref idref="chapter028"/>
    <itemref idref="chapter029"/>
    <itemref idref="chapter030"/>
    <itemref idref="chapter031"/>
    <itemref idref="chapter032"/>
    <itemref idref="chapter033"/>
    <itemref idref="chapter034"/>
    <itemref idref="chapter035"/>
    <itemref idref="chapter036"/>
    <itemref idref="chapter037"/>
    <itemref idref="chapter038"/>
    <itemref idref="chapter039"/>
    <itemref idref="chapter040"/>
    <itemref idref="chapter041"/>
    <itemref idref="chapter042"/>
    <itemref idref="chapter043"/>
    <itemref idref="chapter044"/>
    <itemref idref="chapter045"/>
    <itemref idref="postscript"/>
    <itemref idref="note"/>
    <itemref idref="afterword"/>
    <itemref idref="bibliography"/>
    <itemref idref="footnote"/>
    <itemref idref="bm001"/>
    <itemref idref="bm002"/>
    <itemref idref="bm003"/>
    <itemref idref="abouttheauthor"/>
    <itemref idref="alsoby"/>
    <itemref idref="aboutpublisher"/>
    <itemref idref="Index.xhtml"/>
  </spine>

I.e., the Book Browser display doesn't match the actual spine. Also the spine reference of the item that was moved to the first position (<itemref idref="toc"/>) was deleted. The cover image spine entry (<itemref idref="my-html-cover" linear="yes"/>) was also deleted.

content.opf contained the following guide section:

  <guide>
    <reference type="cover" title="Cover" href="Text/cover.html"/>
    <reference type="toc" title="Contents" href="Text/contents.html"/>
    <reference type="text" title="Start" href="Text/title.html"/>
  </guide>

After deleting it, the bug disappeared.

@RbnJrg If your guide section contains entries, please temporarily remove them for testing purposes, before selecting Create Index and report back whether this makes a difference.

EDIT: You can also use this MR book by GrannyGrump to reproduce this issue.