Junkrat and pharah direct hits technically are two damage instances(direct bonus + aoe) and do not trigger divine intervention when combined dmg is above 125 but direct bonus is under 125. Perhaps this is intentional but feels bad/unintuitive for the avg player imo as I feel it is perceived as a single dmg instance.
Edit: Also upon testing more I found that reaper does trigger divine intervention which is many dmg instances(pellets) reaching the threshold and triggering the item, so I would assume that this definitely is a bug specifically for pharah and junkrat direct hits.