There's something seriously wrong with that roof. No sense in guessing what or why, just have a pro inspect roof decking and frame.

I'd start by looking in your attic. Get up on a ladder in your attic, if need be. If the attic has no floor, get some plywood to put on the rafters.

I agree, with Sigrid, put a couple of boards on the floor joists, if no floor to walk on, and take a good flash light with you, and check out all areas, where you see a depression on the roof. Carefully check rafters, or trusses, which ever your house has. Also check the bottom of the roof sheathing. If anything looks like it could be a problem, then its time, to hire a professional, to check it all out.

"If anything looks like it could be a problem, then its time, to hire a professional, to check it all out. "

And if op doesn't see anything that looks like it could be a problem,does that mean there's no need to bother with a professional?

No, the OP can get an idea of the extent of the issue if he goes in his attic, but either way, something is wrong and needs a pro. My guess is the sheathing was rotted and not replaced, but the OP was probably charged for the plywood. Call your roofing contractor ASAP

But look for yourself first so you know what you are telling the contractor so they don’t try to BS you

Update: last week, framer came and I went to the attic with him. There are three spots of decking which are noticeably depressed (no rot, no crack). Rafters look good. The framer took the pictures and said he would send to the office and let engineer have a look. He preferred to place some 4*2 studs under the depressed areas to provide supports but the engineer may think it is within tolerance. I will update the final outcome later.

You should hire a professional THAT DOES NOT REPERSENT THE BUILDER to advise you if the engineer approves anything other than replacing deck. You might believe houzzers in your corner assures getting a fair deal but that's only "BSing yourself". Telling you to go shimmying around the attic to make sure builder doesn't "bs you" is like telling you to look at x-rays to be certain radiologists are telling the truth.

I am really sorry you are dealing with this Jack. I would definitely get a 2nd opinion on that proposed solution as Klem suggested.

Klem, you had asked if those saying he should go look at his decking from his attic meant he didn’t need a pro. I said, no he definitely needs a pro to assess this problem as it is 100% a problem, and determine the best solution, but he also needs to look in his own attic and see what things look like and educate himself before he just called the roofer. If he saw a or truss or could feel it was wet and rotten, he could call his roofing contractor and tell them specific information. To arm himself with information beforehand. He could even pay another professional to come look first with him sure, but he still should go with that pro, take pics, and he should go look again and take more pics after it is fixed. My suggestion was step 1–go look for yourself, step 2– call a pro. And that was based on what I thought was a new roof on an old house with old sheathing that could be water damaged

Jack, it sounds from your follow up that it is a 1 yr old house? It is reasonable to expect the contractor to make it right, but I am concerned that there is a problem with the structural integrity of the entire roof. Time for step 3–outside consultation. Good luck!

Thanks @klem1 and @rtpaige03. What does the professional/service call related to this? "House framer", "Framing inspector"? I appreciate it if you can help me more :)

You don't need an engineer. You simply need a tape measure, flashlight, small tools, and a notepad. Measure the spacing between the trusses. Verify the thickness and material of the roof sheathing. Compare that to the approved plans, the building code, and all manufacturer's installation instructions.

Normally i would say call another framer or roofing contractor, but Being that your builder’s framer is already consulting an engineer, I would call around to other structural engineer’s in your area for your 2nd opinion. This way you have an apples for apples comparison

I just don't understand the engineer worship here on Houzz. It's like engineers are the be-all end-all of construction. Sorry, these are the subs you hire when you have math to do. They put their pants on one leg at a time, just like us blue collars.

I met a structural engineer in hillside crawlspace and he pulled his little level out of his pocket protector to see if a 50' beam was level. Laughable. Dude, you need a laser or an old-school water leve to get that information.

A homeowner hired an engineer to recommend repairs to trusses compromised by a faulty HVAC installation. His recommendations were silly. 4 pages of "put it back the way it was". Absolutely useless.

Speaking of laughable ,silly and absolutely useless ,try this on for size. OP taking a tape measure, flashlight, small tools, and a notepad. Measure the spacing between the trusses. Verify the thickness and material of the roof sheathing. Compare that to the approved plans, the building code, and all manufacturer's installation instructions.

Is there one amongst us that believes op is capable of determining the problem then going head to head with builder and his tradesmen on how to remedy it? For that matter can anyone think of a remedy that doesn't require deck replacement as determined with a tape measure,flashlight,small tools and a notepad? It's a tear off and replacement of deck at the minimum and possibly framing so why waste time in the attic looking at something he doesn't understand?

klem1:

Any person of average intelligence can gather the information required as I suggested and compare that to the requirements. If the information matches, there is nothing to be done. If it doesn't, that person can see out professional remedies as required.

Joe the ability or lack of ability to do a task isn't a reflection of one's intelligence, it's a product of training and experience. If I had a dollar for things people make worse or ruin with just enough information to get them in trouble I could buy an island.