Is prefetching links worth it on a content site?
On hover, yes, and it is nearly free: by the time the click lands the document is often already there. Prefetching everything visible is the version that burns other people's data plan for a marginal gain.
Is removing Bootstrap from a five page site worth the effort?
Usually yes at that size. Grid and flexbox cover the layout, custom properties cover the theming, and you stop shipping 200 KB to style five pages. The part people underestimate is the component behaviour, not the styles: modals and dropdowns have to be rewritten.
What is the most common way people get this wrong?
Doing it once and never verifying. The setup is the visible part, so it gets attention, and the check that would catch a silent failure never gets written.