Q: Should references be included in a plagiarism check?

References are usually excluded from automated plagiarism checks, as they would naturally throw up a very high percent similarity in the results. While references are always excluded, there's no universally accepted guideline as to what percent similarity is considered plagiarism. This varies from journal to journal, depending on the field of study and the nature of the content. In general, a percentage similarity of 50% or more would definitely raise alarm. This seems to be the general consensus as per a survey of journal editors, published in 2013. However, most journal editors supplement the results received from plagiarism check software with a manual check and human discretion. Many journals also exclude the methods section from plagiarism check as the language used in this section is quite standard and repetitive by nature.

I would advise you to run a plagiarism check on your manuscript, excluding references, and review it very carefully if you get a score of 30% or more. More importantly, ensure that entire sentences or chunks of text are not highlighted by the software, and that appropriate references have been cited for all highlighted parts. 

I hope this helps! Also read our more detailed tutorial on plagiarism.