Found this on the official Marvel Heroes forum.

Jani Kivelä ‏@TavaFIN2h@MMMSociety

Isn't quest to take down Doom supposed give hero that you don't already have, on 1st playthough?

Marvel Heroes ‏@MMMSociety2h@TavaFIN

We know about that issue and we're fixing it. Hang on to the token.

​I hope you guys saved your tokens!

UPDATE:

Crystal ‏@HotHulaChick11m@MMMSociety

Is there anyway to still get the mystery package if I destroyed my duplicated character token? I didnt know it was a bug. :/

Marvel Heroes ‏@MMMSociety11m@HotHulaChick

We're looking at that.

Seems that those who deleted it will most likely get something still.

It's too bad that the only character honestly worth a shit from the base five characters is Hawkeye, maybe Scarlet Witch.

Scarlet Witch is a monster for most of the game, she's just not a great solo.

I wonder if they'll rotate which characters are free at some point. It would be a bummer for people who jumped on the game early but it would also be pretty sad if hub areas were always full of Things and Hawkeyes.

I saw mostly Scarlet Witches myself...

I picked the Thing and literally the first NPC i talked to gave me Hawkeye for free. I assume that's suppose to happen?

I ended up just spending the 10 bucks for Cyclops tho because I liked him in the beta but I really dont' see much difference between characters. From the looks of it, he is just a mix of Iron Man and Captain America perhaps. So I'm good with just spending 10 bucks for one character and getting a full, good game out of it.