I've found another issue in the document: after figure 25, it jumps back again to figure 1 ... adding this because these two figures are in the same section, so the issue does not appear to be related to section breaks.

Anyways, rather than fix I decided it would be quickest to re-do: I just went and manually selected each figure, right clicked and selected "Insert Caption..." and re-captioned everything. That solved the problem (except I now have to fix a bunch of figure references).

Still interested though in knowing about how I would have fixed the original problem!