To be fair, only Lusamine was the evil one--most of the Aether Employees weren't even aware of the Foundation's secondary motivation (which was Lusamine's primary motivation). Like the one Aether Employee at the dock when Gladion takes you there tells you "Things are getting pretty rough here, you wanna go back to Malie City?"

The International Police Force 'KNOWS' about Ub's, and know what they can do to people. The implication is that the ENTIRE foundation (except Wicke) was hit with Nilhilego venom.