I have the quest "A Return to Your Roots" active and it says, "Collect Crimson Nirnroot in Blackreach (-4/30)

To add to this, I've only collected 3 Crimson Nirnroot and just put them in my ingredients chest for the moment.

Well, that's odd. When I put them into a chest it just went back down to zero.

A little math... - 4 + 30 = 26. I hope you can complete that quest.

I'm not even sure what the outcome of that quest is, I've been too lazy to collect 30.

O.o that's weird I would recommend either loading up a auto save if u havent overwriten it or just trying it out and hoping for the best.

You get an ability that will be useful for alchemy.

Forgot how to make a spoiler button or I'd tell you what it is.

You've used one somehow. There are more than you need for the quest though.They may also respawn, not sure. Maybe you miscounted?

You get a passive buff that gives you a chance to produce 2 potions/poisons at once when combining ingredients in Alchemy. It's called Sinderion's Serendipity.
And I would call that bug troll math

There is more than 30 crimson nirnroot and they indeed do respawn.