Thank you for your help Guessed.

Following online instructions for displaying the field code, this is what came up:
{TOC \o "1-3" \h \z \u}

Tried the Ctrl-Q and Ctrl-Space but that didn't seem to work. On some of the headings, the multiple numbers aren't even visible in the document but they still show up as three lines in the TOC.

I kept the headings and proceeded to remove the majority of the text under each, updated the TOC and now it looks exactly as it should. All the multiples lines are gone and there's no repeating numbers in the document anymore.

Does that mean something was wrong with the formatting of the body text? It was all supposed to be 'Normal' styling.