So I recently GMed We Be Goblins. The sessions list for the character I assigned it to shows me earning 2 prestige points for it. Is this correct, or should I have only got 1 like the players?
Follow the rules in the Guide; you get 1 PP. The online system is only a secondary record and has a known issue with GM PP on modules; maybe it will be corrected at some point, but I wouldn't worry about it.
You only get one, it's a mistake with the reporting software because it counts double for GM table credits it applies the PP twice. the chronicle sheet is correct :D
Actually it is because scenarios give 2 PP to GMs, and the software doesn't distinguish between scenarios and modules, especially since there are two kinds of modules, Free RPG Day modules which give 1 PP, and sanctioned regular PF modules, which give 4 PP.