I'm guessing, but to get your headings (1, 2, 3…) to span both columns, you've put them in separate frames. When ID scans a page for paragraphs to include in the TOC, it starts at the top left-hand corner and moves rightwards. It then scans the first frame it encounters for TOC styles. If it finds one, it records it and then scans downwards to find any others at the same distance from the left-hand edge. When it reaches the bottom of the page, it moves rightwards again to look for frames further in, and so on. The frames with your headings must be a fraction closer to the left-hand edge of the page than the frames containing the sub headings and body copy. The 'x' value of the top left-hand corner of the frame is what counts, and even though they may be identical in the control panel, there could be a tiny difference in the fourth decimal place. You might even be able to see a misalignment if you zoom in as far as possible. Try nudging the headings a point or two further right and see if the problem doesn't go away.
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