Here the original after was very probably a conjunction rather than a preposition, which means that the that should have been deleted in the editing for the 1837 edition (see the discussion under 1 Nephi 1:17, plus the general discussion under subordinate conjunctions in volume 3). However, the 1830 typesetter placed a comma after the that, which means that he interpreted “after that” as a completed prepositional phrase. The original text apparently intended to say that after being in captivity to the Lamanites, the people of Alma were once more delivered out of bondage by the Lord. Note that just previously (in verse 4) the text refers to the first deliverance of the people of Alma: “they were delivered out of the hand of the people of king Noah by the mercy and power of God”.
What we have here in Alma 5:5 is a Hebraistic and between the subordinate after-clause (which includes a parenthetical yea-clause) and the following main clause (“again the Lord did deliver them out of bondage by the power of his word”). For further examples of this kind of usage with after-clauses, see under Alma 3:1; also see the general discussion under hebraisms in volume 3. The critical text will therefore remove the comma after the that in Alma 5:5. Suitable editing for the standard text, consistent with Joseph Smith’s editing for the 1837 edition, would be to delete the that (as well as its comma) and remove the and that occurs before the main clause, thus giving “and behold after they were brought into bondage by the hands of the Lamanites in the wilderness—yea I say unto you they were in captivity—again the Lord did deliver them out of bondage by the power of his word”. For another example where “after that” was interpreted as a completed prepositional phrase, see Ether 4:3. There are, of course, actual examples of prepositional “after that” in the text:
Summary: Remove in Alma 5:5 the comma that follows the subordinate conjunction that, thus restoring an original Hebraism to the text (namely, an instance of and between a subordinate after-clause and its following main clause).