I apologize if I should be posting this question elsewhere, but I've had no luck finding an answer as of yet.

While working on the Frontal Assault quest, I had no trouble getting the Whisker Purchase Order from the boss in Not the Mutant Operations Center. The whisker boss in Not the Rumored Refinery isn't being so nice about dropping the Mutant Work Receipt, though. I've killed him several times now, and he drops loot, but no quest item. Am I being a huge noob, or is the quest wonky?

I'm not familiar with that quest in particular but if you've killed him a few times and he hasn't dropped the quest item then it could very well be bugged.
You might try fighting him on Insane if you weren't already.

I'll give that a shot, then. Thanks for the help!

Update: On a hunch I went back to the Not the Mutant Operations Center to see if one of those bosses had the work receipt, and one did. If I did the refinery last night and not the MOC like I'm thinking, then the quest item locations might just be backwards. Either way, all's well that ends well.

Glad you got it sorted out mate.