I've played around with a few chars now and the same is happening for all. The tracker hasn't been updating when filling Phials for quests. Mostly in the Night Elf starting area.

When I look at wowhead for this quest (ID 933), it seems to have an extra "Explore Zone" requirement.

https://www.wowhead.com/wotlk/quest=933/crown-of-the-earth

When you search for "Crown of the Earth", and hover your mouse over the quest, it says "- Alexston Farmstead" as a second requirement:

https://www.wowhead.com/wotlk/search?q=crown+of+the+earth

It seems to be an old relic that there's a hidden requirement to explore a part of Westfall, but it's not actually required. I assume that's why Questie doesn't see it as complete with the current data.

The same goes for the following quests in the chain:

https://www.wowhead.com/wotlk/quest=921/crown-of-the-earth
https://www.wowhead.com/wotlk/quest=934/crown-of-the-earth
https://www.wowhead.com/wotlk/quest=929/crown-of-the-earth

I would say the simple solution is to remove the "Explore zone" requirement in Questie's data for these four quests

out of curiosity, if oyu have one of those quests (or can get one) can you fill the vial and then do a different quest, or advance another quest? then check the tracker.. if it is still not showing the filled vial then try a /reload to see ifthat works.
thanks for testing

Reloading worked I think. I don't remember if it showed 1/1 Filled Phial or whatever.

This was after reloading.

Works fine after turning in the quest, before the next step.

Just started doing this I think after the last 2 updates.

I also noticed that sometimes the Tracker simply does not update correctly but only on either the next time you enter+leave combat or another quest updates comes it.

I didn't find a pattern yet.