Remove all numberings, which were set by such buttons. The buttons are for list numbering, not for chapter numbering. Format your headings with style “Heading 1”, “Heading 2”, … Goto Tool > Outline numbering in the master document, make sure these styles are selected, and choose the kind of numbering. With this defaults, numbering in TOC will work out of the box.
If you have assigned a style to the outline level in Tools > Outline numbering, then the button will switch on/off outline numbering when your cursor is in a paragraph with this style. If your cursor is in paragraph which has a style, that is not used in that Outline numbering dialog, then the button switches on/off list numbering.
Set the cursor into the heading. The status bar tells you whether the numbering of the heading is OK:
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Outline Numbering: Level 1 → OK. But you might need to reload the document to get the numbers correctly counted.
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Level 1, Outline 1 or Level 1 → That is a list numbering. You can remove it by Format > Bullets and Numbering > Remove, or by the button Numbering on/off, or by key F12.
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Outline → The heading has a direct formatting to not show numbers. Format > Clear Direct Formatting.