A family of Microsoft word processing software products for creating web, email, and print documents.
Since your description doesn't actually mean anything in Microsoft terms, perhaps you can better explain what you're doing. You've used the ruler to set tabs and indents in TOC entries, perhaps? Because the TOC styles are set to update automatically, this will result in modification of those styles, and they will stay modified unless you modify them again.
But if you're asking how to prevent the TOC from updating and wiping out manual formatting you've applied, then the only way is to lock the TOC (Ctrl+F11). You will not be able to update the TOC unless you unlock it (Ctrl+Shift+F11), and unless you update only page numbers, your direct formatting will be removed.
Perhaps if you tell us what you're trying to achieve, we can help. You might also see http://wordfaqs.ssbarnhill.com/TOCTips.htm for information on formatting a TOC.