When upgrading multiple things in the covenant hall at the same time only the first upgrade started will complete, while the others will be cancelled without refunding the anima and souls spent on them.
Lost 44 souls and 20k anima attempting to upgrade venthyr transport network, anima conductor, and command table top level 3 all at once, where only the transport network that I had started upgrading first finished and the other two were cancelled.
Ive just done the same thing on an alt and all 3 upgraded correctly, so I would raise a ticket about it if I were you.