Near the end of verse 5, Joseph Smith deleted “it came to pass that” because nothing new had come to pass. This instance of “it came to pass” actually restates the fact that the preceding list of complaints was given before the chief judge of the land:
And because the example of “it came to pass that” in verse 5 was deleted, Joseph also deleted in the following verse the also that occurred immediately before the next “it came to pass”.
Joseph Smith made two other (more stylistic) changes in verse 5 with respect to the (original) first occurrence of “it came to pass”: (1) he added now after the initial and, and (2) he replaced the following subject pronoun it with this. In other words, in the printer’s manuscript Joseph changed “and it came to pass that it was done before the chief judge” to “and now this was done before the chief judge”. The 1837 edition, however, ended up omitting the sentence-initial and, giving “now this was done before the chief judge”. This last change could have been intentional since elsewhere the text consistently prefers now over and now before “this was done” (although one wonders how sensitive editors or typesetters would have been to such stylistic nuances in the text):
The critical text will, of course, restore the original text here in Alma 14:5–6. The original text had cases of supposedly unnecessary uses of “it came to pass”; for discussion, see under 1 Nephi 10:17 as well as more generally under come to pass in volume 3. The other changes introduced in the 1837 edition for this passage are simply stylistic.
Summary: Restore in Alma 14:5 the original “and it came to pass that it was done before the chief judge”; also restore the original also in the following verse (“and it also came to pass that Zeezrom was astonished”).