I recently submitted my replies to peer review to a journal. After submission I found out I had missed out on turning on track changes to the last part of my manuscript. Will this cause a problem? Do issues like this irritate journal editors and reviewers and lead to rejection of a manuscript?
Did they specifically ask for change tracking to be turned on? If so, then you should contact the editor and send in an updated version that meets their requirements. If not, then don't worry about it.
Having to handle additional versions due to an author's mistake could be a little irritating to an editor or reviewer, but if they're expecting change tracking, then it would be more irritating not to have it. Anyway, administrative issues like this, which do not affect the content of the paper, should not be a reason for rejection.
The editor may be irritated or not, but that shouldn't concern you. What you should do, however, is immediately send a corrected version with an apology. The apology should be sincere, but needn't be overly long or explanatory.
If it will take you a few days to get the manuscript ready, then immediately send an email if you can with the apology and the date he/she can expect the revision.
The editor would like to correct it quickly so as to avoid too may turns between you and the reviewers. They are interested in publishing a high quality manuscript, not in punishing authors.