Here we have two instances of variation involving the possessive pronoun their. In the first instance, we have a case of the singular pronoun his in a generic clause: “whomsoever shall put his trust in God”. But since the following text uses the plural generic pronoun their, Joseph Smith emended the earlier his to their in his editing for the 1837 edition. As explained under Alma 32:25, the original text allows (under certain conditions) mixtures of the generic pronouns he and they. The critical text will restore the original use of the generic his here in the nominal clause “whomsoever shall put his trust in God”.
The other instance of variation here in Alma 36:3 involves the repetitive their in the conjunctive phrase “in their trials and their troubles and their afflictions”. When Oliver Cowdery initially took down this phrase in 𝓞, he omitted the final their. But almost immediately, he supplied it by supralinear insertion (there is no change in the level of ink flow). Such multiple repetition of the possessive pronoun is found in another instance of this same conjunctive phrase (namely, later when Alma talks to his second son, Shiblon): “ye shall be delivered out of your trials and your troubles and your afflictions” (Alma 38:5). The critical text will, of course, maintain the multiple repetition of the their in Alma 36:3. For further discussion, see under conjunctive repetition in volume 3.
Summary: Maintain the repetitive their ’s in Alma 36:3 (“in their trials and their troubles and their afflictions”), but restore the original his in the whomsoever- clause (“whomsoever shall put his trust in God”).