I have a habit of biting the side of my cheek, On shabbos, would this habit be considered breaking shabbos?
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If you're making it bleed or bruise it could be a problem; (the labor category of "slaughtering" includes any causing of bleeding), otherwise, I don't see the issue.
If you are doing it out of habit (i.e. unconsciously) then even if it makes it bleed this might be considered misaseik (unintentional) and may not be something you are guilty for doing, even though it is recommended you break the habit.