Hi Chenrong,
I remembered using AutoMPO to make Hamiltonian with two operators on the same site myself before and it didn't cause any error, and I have seen others doing the same thing without any error on this forum, have you checked that you had the latest version of ITensor package? On the other hand, maybe you could use "Nup",2 instead of "Cdagup",2,"Cup",2 or make a new operator to represent the two operator on the same site.
Best,
Yixuan