Minor typos found directly after submission of a revised manuscript to a geochemistry-focused journal
These errors should not lead to rejection. Even if the paper will be accepted now (i.e. no additional round of revision) there will be a chance to correct those errors during proof-reading. The missing reference will probably be detected by the journal and corrected automatically.

Take notes of the errors, so you can be quick once you get to proof-reading stage, since often, publishers give you as little as 24 hours to check and correct a manuscript.

I just remember that there are fields where the authors take care of formatting and editing of the final version - there things might be a bit different. My  answer is based on journals that do the editing for you, after acceptance of the manuscript.



The fact that your supervisor (or any corresponding author) submitted a (revised) manuscript without asking co-authors and making sure, they approve the manuscript, is a different matter and should not have been done. Look for posts regarding "submitted without consent/approval" to find out more (basically, the corresponding author has to make sure that all co-authors have seen and approved a manuscript before submission, at every stage).