The widgetVar basically generates a window scoped JavaScript variable. What you're effectively doing now in JavaScript context is:
window['whatever'] = new Widget(lightboxElement1);
window['whatever'] = new Widget(lightboxElement2);
window['whatever'] = new Widget(lightboxElement3);
// ...
This way the whatever variable in JS would only refer the last one.
You should basically be giving them each an unique name, for example by adding the iteration index:
<ui:repeat var="thing" value="#{bugBean.things}" varStatus="iteration">
<p:lightBox widgetVar="whatever#{iteration.index}">
This way it becomes effectively:
window['whatever0'] = new Widget(lightboxElement1);
window['whatever1'] = new Widget(lightboxElement2);
window['whatever2'] = new Widget(lightboxElement3);
// ...
This way you can refer the individual lightboxes by whatever0, whatever1, whatever2, etc.
Unrelated to the concrete problem: isn't it easier to use a single lightbox and update its content on every click instead?
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