Making additional changes to manuscript after the refereeing process is completed
I always make minor edits (unrelated to the reviewer comments) at the time of doing revisions, and make a comment in the response letter, e.g. "we have also made minor changes to improve the readability of section 4.2." It's in the interests of the journal to have a well-written article. 

Depending on the journal, you will probably also have a chance to make very minor revisions during the copyediting process.