Here scribe 2 of 𝓟 originally wrote the singular affliction (miswritten as afflicton). Perhaps he was influenced by the preceding occurrence of was (thus “and so great was their affliction”). Scribe 2 corrected the singular afflictions to the plural by supralinearly inserting the plural s. (The s itself is written with somewhat heavier ink flow, but the insert mark itself is not; perhaps scribe 2 redipped his quill in the middle of his correction.) The plural afflictions was probably the reading of the original manuscript.
The original text clearly allows plural subject nouns to occur after a singular form of the verb be, as in these two examples with the phraseology “so great was X”:
The second of these has afflictions as its plural subject. More generally, the text allows examples of both singular affliction and plural afflictions; see, for instance, the discussion of the phrase “great affliction(s)” under Mosiah 11:27. For a general discussion, see under subject-verb agreement in volume 3.
Summary: In Alma 4:3 the plural afflictions should be maintained; in addition, the singular verb form was will be restored in the critical text (“and so great was their afflictions”).