When a BHS footnote (to the critical apparatus) comes between two words, it appears to be counted as a word, which means two words in sequence are no longer found by the THEN operator.
For instance, in BHS Dt 11:2, we read "(object marker)(a)–his greatness and his outstretched (b) arm," where (a) and (b) are footnotes. When I search for the Hebrew lemmas corresponding to "outstretched" and "arm" with the operator THEN or "WITHIN 1 WORDS", this verse is not found. These words are separated only by a footnote. When I broaden the search to "WITHIN 2 WORDS" the verse appears. The hebrew in question,"וּזְרֹעֹ֖ו הַנְּטוּיָֽה׃" includes a nominal suffix on the first word and the article before the second word, but this should not cause the words to be counted as separated, and other verses with both those features appear in the search, e.g. Dt 9:29; 1 Kgs 8:42.
The same problem appears with the search for (object marker) THEN "arm," again using the Hebrew lemmas, the same problem occurs, leaving out Dt 11:2 and including the many other verses with the same text, including again, coincidentally, 1 Kgs 8:42. The object marker and "hand" are not counted as subsequent words even though they are joined with maqqef.
I have included a screenshot in which both searches can be seen, along with these two verses, Dt 11:2 and 1 Kgs 8:42. The precise search strings I used are lemma.sesb.h:זְרֹועַ THEN lemma.sesb.h:נטה and lemma.sesb.h:אֵת.1 THEN lemma.sesb.h:יָד
This problem does not seem to be caused either by the critical marks in NA28 or footnotes in RSVCE2; that is, those texts return the search results I would expect with the THEN operator.