With BookDesigner it can be a hit-or-miss thing. Sometimes it works fine and other times it will (on its own) decide that certain text lines are TOC elements. In most cases it is easy enough to correct these problems using 'Element Browser' under the Tools menu item. There is also a facility in BookDesigner that I use for generating the TOC -- under the Insert menu is 'Insert TOC (all)' that places a TOC at the start of the file just after the title and author. (It can be moved.).
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