If you’re using the unsrt bibliography style, you’re expecting that your bibliography will not be sorted, but that the entries will appear in the order that they first appeared in your document.
However, if you’re unfortunate enough to need a citation in a section title, and you also have a table of contents, the citations that now appear in the table of contents will upset the “natural” ordering produced by the unsrt style. Similarly, if you have citations in captions, and have a list of figures (or tables).
There’s a pretty simple “manual” method for dealing with the problem — when you have the document stable:
auxfile, and any of
The package notoccite avoids the kerfuffle, and suppresses citations while in the table of contents, or lists of figures, tables (or other floating things: the code is quite general).