When I first got to the Nexus almost right away in the DLC. I noticed a side quest marker off to the right that didnt seem like it was possible to reach yet. It looked like I would open the area later. After doing the Fyrestone stuff I go back to that area and there is two new side quests to accept from the mini claptrap and the drunk looking one. But that other one is gone…what is up with that?
The only other side quest I can immediately think of is the “russian spy” thing, where you need to hand over 200 moonstones. I don’t believe you can miss it - generally, the BL games don’t include missable side quests (although there are missable challenges). IIRC, some of the Nexus side quests cannot be picked up until a certain point is reached in the main story progress; that’s about it, really.