GRE incorrectly assessed as Testamentary Trust

I have a T3 Return for a GRE that CRA has assessed as a Testamentary Trust. When I talked to an agent today she said that the estate is set up as a testamentary trust and not a GRE. In looking at my T3 returns in TaxCycle, I have it set up as a GRE and told the agent that. She then said it would have been from when I registered for a Trust number. I have the submission confirmation from that which also shows I registered the Trust as a GRE. They also keep asking me if I prepared schedule 12 (I did not). However, the trust had a rental property, so a T776 was completed. They said some of the issues with how CRA assessed the Trust had to do with the fact that there was an amount in line 12050 on S12 (appears to be from bank/interest charges from T776 that flowed here). When I look at the tab in TaxCycle for S12 it is a blank white paper, which I think means that it was not a prepared/in use schedule and it does not show up in my print set. So I don’t know why CRA has it…
I am trying to figure out what is a CRA caused problem vs a software issue.

The agent said that we will have to send a letter requesting the Trust be changed to a GRE and that the return be reassessed as such. But should this be done as a notice of objection?