Should references in the supplementary information be included in the main text?
Citations that do not appear in the main article should not appear in the bibliography section of the main article. Instead, you should create a separate references list in the supporting information, and use a separate numbering scheme. Usually you can use the same numbering scheme as in the main article; it will be clear that references apply to the supporting information, rather than the main article. (You could add a footnote to that effect if you want to make this clear, since supporting information is usually handled "as is" by the publisher.)