Here Joseph Smith, in his editing for the 1837 edition, decided to delete not only the repetition of “it came to pass that” in this verse but also the repeated subject noun phrase, “Moroni and his army”. The critical text will restore both repetitions since this is clearly the earliest reading (in both manuscripts as well as in the 1830 edition). Joseph also deleted the subsequent instance of “it came to pass” (in the next verse):
Sometimes Joseph removed multiple occurrences of “it came to pass that” when they appeared close together in the text. See the example discussed under Alma 8:18–19 as well as other examples listed under come to pass in volume 3.
Summary: Restore the original instances of “it came to pass that” in Alma 43:41–42 that Joseph Smith deleted in his editing for the 1837 edition; also restore in Alma 43:41 the repeated subject, “Moroni and his army”, which Joseph also deleted.