The mission tracker on the right side of the screen is bugged. As a mission is being completed, such as an item being obtained out of however many, that mission won't go to the top. It will stay in the same place and actually makes leveling just a tad annoying and difficult to manage when there are a lot of missions for me personally.

You need to hit the J key, or whatever you have bound for Mission Journal.
Then select a mission and 'set primary'.
This puts that mission to the top of your right column quest list.

Yeah .. but the Tracker is still bugged, since for long time the missions always went automatically on top
when they get an update, and that was good when you have maybe a full journal and 3-4 missions that
gets updates in the same area, since you can only set one primary mission.

Yesterday i also noted that the bug doesn't seem to affect ALL my character, on some it still works but on
others not. I already searched through the options if there is somewhere a switch for it, but didn't found anything :o

If it automatically moves things to the top you'll never know what mission is primary.

There's no way for team leader to keep five people in synch if everyone's top line mission is flipping
around randomly by picking up a purple hat, or defeating a cobra, or grabbing a weapons case, or
taking down prisoners, or finding the super jet.

Also if you Hide a slew of missions, then seeing status on active and local missions is easier.
However the list visibility settings reset on zone changes.

The primary always stays on top, but other missions went directly to the second position if you have a primary
and on top if you have no primary

Yes definetly fix this, I keep having quests that are taking place in the area I'm in that I have to keep opening the quest log between fights to see how far along I am.

I agree, it's pretty annoying and makes leveling feel somewhat clunky. :(