When I start a new save and new character a bunch of the missions are already done for me. Is there a way to clear this or what would I do if I were to do a gen2 run?

had the same problem on my run, looks like just a visual thing.

for runs: if you wanna be save - show the effect tab and leaderboard tab if both are empty theres no problem as longs as you complete all the missions in the run i dont see a problem there, its ARK...

Okay I'll just make sure I do those ones.

Now that I took a closer look at these missions I think this was done on purpose. All the completed missions are hunt missions and the tranq missions. The tranq missions are basically impossible on alpha and hunt is just really hard. This is probably a temporary fix until wildcard fixes the missions.