What is "renovating"? What does it need? Do you want to change something?

It looks like you should have held off on the reroof until the structure was repaired.

Your house is stucco?

What type of roof is there now? What was there before?

Hi yes it’s stucco. The roof type is the same as before, it was liberty self adhering roof
The structure needs repair but I’m not sure what that entails.

Well the repair entails ripping off the roof, decking, and crown and replacing whatever else is damaged. The roofer should have told you that you weren’t ready for him yet

Yeah, the roofer did you no favors. You did this out of order. Structure must be repaired and rebuild first, then the roof.

Just another example of incompetent and indifferent contractor we see much too often. If consumers don't raise the bar, it'll never improve.

It's probably too little too late but you have nothing to lose by bringing this to the attention of your code enforcement office and ask if roofer holds required credentials. Adding insult to injury,that "rectangular piece" looks like a sick joke.

Please let us know what city officials say about it.

Thank you all so much for the advice. It’s so frustrating to know that the contractor should have shared this information and was not transparent with us. I really appreciate the guidance.