Created attachment 215310 [details]
HTML file highlighting the problem
The CSS 2.1 spec says that elements that are not displayed and don't generate boxes (e.g. elements with display: none or children of such elements) do not increment counters.
The CSS Regions spec implies that children of regions or named flows without an associated region chain are in nature the same as elements with display: none.
However, setting counter-increment on elements in a named flow without an associated region chain still increments the counter.
E.g. in the attached file, the three elements should be numbered 1., 2., 3., but they are numbered 2, 4, 6 . Replacing flow-into/flow-from with display: none produces the proper numbering (1, 2, 3)
The bug also reproduces with numbering generated by <ol> elements.