Unfortunately without a lot of knowledge on the topic, it will be hard to tell if things are done correctly or not. However with the items you mentioned, I would certainly not accept smaller windows as an option.
Looking at walls is also fairly easy to know if they were framed right. Sighting down a framed wall you can fairly easily see if there is wave in it or not. A common mistake made is they do not crown the studs prior to framing. This is what makes that wavy look you are talking about. However unless they are really bowed (which should not be used anyway) wave in a finished wall will be hard to see.
Where did the plan come from? Builder? Architect?
If you do not have an architect or someone else to inspect, I would just recommend to keep studying the plans. Check measurements if you can get onsite without them there. If you find mistakes, confront them in a good manner. For example, if I find or think there is a mistake, I do not say this is wrong, rather ask can you verify this for me?
You should not have a babysit the professional you are paying, but sometimes that's the rare game that has to be played.

We ordered the plans from an architect. The small cottage was published in Southern Living and we contacted the architect. He emailed the plans to us, so he is not here to ask questions or check on work. We are pretty much on our own. The plans are extremely detailed, though. Will it cause a structural problem to have them redo the headers to the plans (3 2x8's) rather than the 2x10's they already have everywhere? Whatever they did shortened the height from bottom of header to the floor by 4". Thank you so much for your advice!

Without knowing the opening size and the loads on them, I can not comment on the headers. However if the plans call for 2x8 and they used 2x10s, then no, there is issue there as the headers are actually stronger than your plans. They could cut the headers down in place to 2x8 if they wanted to. Not knowing your climate, the 2x8s would have been the correctly sized headers I assume, but I typically go with a 2x10 or 2x12 box header and insulate the inside of them anyway to cut down on the massive thermal bridge above the windows.

I dunno, but perhaps it's time to stop the construction, have a meeting and ask the builder why he isn't following the drawings you bought?

Just a thought.

"Just a thought."

In my opinion the only thought.

ditto....I can't believe a 'professional' would make so many mistakes like that in the beginning. Is the GC the actual framer with his own crew or is it sub out? Either way, stop everything.

Thank you so much for the great advice. The GC has his own crew. We thought he would be using them; however, he sub'd out to brother, who we know also. (It's a small town). We met with the GC yesterday. When we asked why the framers weren't following plans, he told us that is how they normally frame headers and that they were actually better than what plans call for - except the windows won't fit and transoms above doors and windows won't line up at the top across the front and side of the house. To be honest, I think the framers were rushing, just did what they always do, weren't reading the plans, and didn't think it would make a difference or that we would know the difference. When getting bids, one contractor told us we didn't need to waste money on plans - that they could go by the very basic floor plan you can print off the internet. And he is the other contractor that comes highly recommended in the area. I trust the plans drawn by the architect. Researching him online, he is very reputable. We put in a call to him this morning and he was very extremely helpful. After your responses and speaking with architect, my husband & I have decided to have him redo the headers to plan and have emphasized that they are to actually use the plans we purchased instead of for decoration for his truck dashboard. I didn't really say that last part, but am learning that I have got to be a lot more assertive even though I really like the GC personally. He is pulling his crew on the job and has apologized. My question now is who pays for mistakes? When they poured 5 yards too much concrete for porch that is sitting out in the yard, shouldn't the framer who made the mistake have to eat that concrete cost? And if they need more lumber to correct headers, shouldn't they have to pay for that or at least rip down the 2x10's they used to 2x8's instead of us paying for more lumber? Should we deduct that as we are paying him now for materials or when we pay his cost plus payment at the end? The contract specifies to be built to plans provided and I even had contract retyped with the architect's name and plan number before we started any work. Thanks again for the advice!

We have had a good experience with our builder so far, but we are all human and there have been a couple fairly big mistakes. Our builder has been the first to say they will eat the cost to correct the mistakes and it has shown up as a credit on our bill for that period (at the beginning of each month, we get a bill with the cost of materials/labor and the GC fee for work completed the prior month). To me, this speaks volumes for the integrity of the builder. On the flip side, if I see a mistake, I really give some thought to whether I care enough about it to have them correct it or whether I just let it go.

Everything the framers installed incorrect(not according to plans), the GC should cover the costs, lumber and labor to fix. Not sure I understand about the framers and concrete. Why would the framers be involved with concrete?

Construction should be very simple: use the drawings and specifications for bidding and construction. Period.

If the builders don't it's their bad and their mistake to correct. On their nickel.

It doesn't have to be complicated.

Good luck on your project. Remember--it's YOUR project.

@robin0919 - the framers "strung off" the house footprint & where the footings were to be dug and did incorrectly. The GC caught the mistake after the footings had been poured. It cost us about 5 extra yards of concrete.

Unless you have a contract with a particular sub-contractor, responsibility for all aspects of the project belong to the GC alone. The GC should give you a credit for the cost to correct the work then it is up to him to ask his subs to reimburse him if they were at fault.

It is difficult to oversee your own project especially when you are not experienced in this field and you know the contractors. If an architect was involved in the construction phase, you would probably not know about these mistakes until a construction directive was issued and a credit appeared on the next invoice.

Make sure the correction will work. The difference in height between 2x8's and 2x10's will not account for a 4" discrepancy.
Three 2x8's will span a pretty large opening but that span will be reduced if it supports a floor and roof. Make sure the architect designed the headers to meet the code used in your area. Three 2x8's are less strong in bending and deflection than two 2x10's and use more wood. Two 2x10's in place of three 2x8's also allow insulation to be placed in the cavity. So, it would be quite rare for a builder to use three 2x8's if two 2x10 were required but that is no excuse for ignoring the drawings. The question I would ask the architect is why didn't he raise the wall top plate 2 inches and save wood and energy?

The first time I supervised a house the French Canadian roofer refused to install underlayment. He sent his English speaking son down to ask me why building paper was needed. To avoid an argument about roof design I told the boy that if he did it he would be paid. He turned and yelled to his father in French and the underlayment was installed. I was glad I couldn't understand anything they said after that.

This post was edited by Renovator8 on Tue, Jan 7, 14 at 11:05

@renovator8 - they also had a 2x6 flat under the 2x10 making up the 4 inch difference. I hope that makes sense.