Necropolis Defender Upgrade Bug

So I’ve got the Neceopolis Defender from the chest in the mission where you get Emmrich, I finished Pinacle of its kind mission and finished Desperate in Dock Town as well, I’ve got the upgrade for the shield in Desperate in Dock Town but didn’t get the one from beating the formless one in Dock Town in Pinacle of its kind, it’s there anything I’ve missed? Because I’ve googled everywhere and I’m certain I must have 3 upgrades already but my Necropolis Defender is only rare level, has this happened to anyone else?