One of the first missions doesn't complete?

I’ve just begun playing, and the game has given me a mission where I must upgrade my railgun. Problem is, I upgraded it before accepting the mission and the next upgrade to the railgun requires loyalty(?). Have I locked myself out of the beginner-level missions or is it supposed to be a more of a long-timed quest?

Those quests on the side aren’t that big of a deal. The “Contracts” are what matter.

Before 0.9.8 mission passed just if you removed that already upgraded railgun from ship (drag it out of slot) and install again.