Found that if you have more than one of the BOA unique trinkets and they are both best, AMR will suggest a BOA 110 trinket for both Slot 1 and 2, which is not actually possible. Also finding that because it cannot equip that second trinket, it doesn't save the current set in the Equipment Manager.
Current workaround is the delete the extra BOA trinket from your inventory, bank, etc.
A similar issue occurs when trying to equip a set that does not have an artifact weapon (Such as when you're 100-102 in a different spec than your main). It doesn't save in the equipment manager.
(Bonus points, is there a known issues topic yet?)