PLOS Computational Biology specifies including [Internet] after the title for specific types of references:

• New media (blogs, web sites, or other written works)
• Databases and repositories (Figshare, arXiv)

For other types, examples do not include [Internet], such as:

• Accepted, unpublished articles
• Online articles
• Books
• Book chapters
• Deposited articles (preprints, e-prints, or arXiv)
• Published media (print or online newspapers and magazine articles)
• Masters' theses or doctoral dissertations
• Multimedia (videos, movies, or TV shows)

Note that arXiv is listed under both "Databases and repositories" and "Deposited articles", although I think the later is a more accurate categorization for preprints.

Currently the CSL Style for PLOS Computational Biology, which inherits from PLOS, places [Internet] after many reference types that fall under the later categories above. It seems that the presence of a URL in the CSL JSON is sometimes used to determine whether [Internet] should be added:

Note that most citeable works these days have a URL, but that doesn't mean they fall into the internet categories above.

We noticed this issue when creating this reference list. Notice the following examples of how CSL JSON was converted to a reference.

csl json: type is entry, but switching to book does not remove [Internet]:

1. Nielsen M. Reinventing Discovery [Internet]. Princeton University Press; 2011. doi:10.1515/9781400839452

csl json. Type is manuscript for a bioRxiv preprint:

10. Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, et al. Opportunities And Obstacles For Deep Learning In Biology And Medicine [Internet]. Cold Spring Harbor Laboratory; 2017. doi:10.1101/142760

csl json for an arXiv preprint where type is report:

15. Phillip Lord, Lindsay Marshall. Twenty-Five Shades of Greycite: Semantics for referencing and preservation [Internet]. arXiv. arXiv; 2013 Apr. Report No.: 1304.7151v1. Available: https://arxiv.org/abs/1304.7151v1

csl json for report type:

25. National Information Standards Organization. ANSI/NISO Z39.96-2019, JATS: Journal Article Tag Suite, version 1.2 [Internet]. NISO; 2019 Feb. Available: https://www.niso.org/publications/z3996-2019-jats