Same issue with me, although I ended up deleting the scout rifle, as I assumed I could grab it from my collections. I have the Polaris Lance, so I had to of had the scout rifle at some point. I'm gonna try and do the quest again on a different character to see if acquiring it will count.
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i lost my Braytech RWP Mk 2 from collection too after 2.1.0 !!! WTF bungie, this is ur fix: -Fixed an issue where the BrayTech RWP Mk. II Scout Rifle was not counting towards Collections for some players.