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Even if I change #4 or #5 to something else, it still the same, #5 indentation is always wrong.

It's an IEEE template.

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    Welcome! As you can imagine, this is not a regular feature, but more information is needed to diagnose your problem. Make a short but runnable version of the document that also has the same problem. From the bit of information shown I can see a subscript in the web address in ref 4, which suggests you got error messages there that reveal the cause for the loss of indentation. All your doi urls have the same problem. Try searching for "url bibliography bibtex latex". Sep 16, 2020 at 3:27
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    You wrote, "It's an IEEE template." The IEEE provides lots of templates -- which document class and which bibliography style do you employ? Also, please indicate whether you load the url, xurl, and/or hyperref packages.
    – Mico
    Sep 16, 2020 at 4:37

1 Answer 1

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@DonaldArseneau, I think that's the reason. Thank you.

@incollection{Chaum1991,
  doi = {10.1007/3-540-46877-3_41},
  url = {https://doi.org/10.1007/3-540-46877-3_41},
  year = {1991},
  publisher = {Springer Berlin Heidelberg},
  pages = {458--464},
  author = {David Chaum},
  title = {Zero-Knowledge Undeniable Signatures (extended abstract)},
  booktitle = {Advances in Cryptology {\textemdash} {EUROCRYPT} '90}
}

As you can see the URL contains an underscore _, and it was rendered as a subscript. Almost all of my references contain the _, that's also why no matter how I move it around, I still have the problem.

Change it to \_ solve the problem.

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    Many styles can interface with the url or hyperref package, in which case it might be enough to load \usepackage{url} or \usepackage{hyperref}. Generally, I'd try to avoid LaTeX-escaping special characters in url fields in .bib files, since they are usually supposed to contain the URL verbatim without change.
    – moewe
    Sep 16, 2020 at 5:52

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