The first thing to decide is if you want to use endnotes (all your references at the end of the book) or footnotes (all your references at the bottom of the relevant page). Having tried footnotes when publishing Golems, Vampires and Wanderers: Essays in Gothic Fiction, I can honestly say that endnotes are easier.
With endnotes, the references are collected all together and can be treated as a separate chapter. The headers and page numbers are dealt with exactly the same. The only additional work is to check the numbering has carried across correctly, and the formatting is correct.
With footnotes, a change is made to the content of potentially every page. The extra text they add will bump the text at the bottom of the page onto the next one. This could have an impact on which page the next chapter starts on, so each chapter will need to be checked to make sure it still starts on the correct page. As with endnotes, check the numbering is correct. One thing I found was that sometimes the footnote would be on the incorrect page to the number in the text, usually the one after. If this happens the only remedy I found was to reformat the text to bump the number in it to the next page. Obviously this will leave you with some very noticeably odd formatting if you later change the font or trim size so it's best to make a note of these places so you can check them later.
Something else that sometimes happens with footnotes is an extra line can appear between them. I have no idea what causes this, and the only way I found to fix this was to manually tweak them until they look right. Footnotes will need to be carefully checked before committing the final file to print, so if your chosen printer offers a pdf print file for checking, take a close look at this as it's how your finished book will look.
Next, ISBNs.