Contact your HOA and the builder as soon as possible. If your covenants aren't enforced and the residents have knowledge of an exception that is allowed to occur, you only have so long before your ENTIRE set of covenants are null and void. Covenants can't be selectively enforced.
We've been going through a three year battle with zoning and now finally a court case in order to try and deal with an issue in our development, so I've become more knowlegable than I'd like to about neighborhood covenants and zoning issues.

Check with your building dept. Who issued the permits and why? Were they aware their is a covenant? Just talked to DH, retired BI, and he said that sometimes they don't know about the covenants and it is not their problem, it is zoning. Grey area. I would say it is the job of the officers/members to find out. Have a meeting to clarify rules, laws and enforcement. Who enforces the rules.

I am president of our neighborhood's HOA. When we had this exact thing happen, I contacted the builder directly informing him of the convenants and asking him if he was planning on enlarging the house. He wasn't. So I contacted an attorney, who, for a fee, wrote him a threatening letter. Our HOA felt it was imperative to enforce each and every convenant, but especially those governing new construction. The builder added on to the house. We had enough money to bring a lawsuit and, by golly, we would have done it. Your first step is to contact your HOA's architectural director, or, if you don't have one, its president. They will take it from there. If they refuse to do anything, all the future builders (especially this one!) will receive a message that these covenants aren't worth the paper they're written on. It would be bad news for your neighborhood.

Don't owners or builders have to get approval from the Architectural Control Committee before they are allowed to build? We can't do diddly in our subdivision without written approval from the committee. I can't see how anyone could build a house 200 s.f. less than what the rules require. If anyone can plop a house in without getting a approval, you need to change your CC&Rs. Easier said than done, but it sure needs to be done. Plus, rules with teeth, fines for every day the correction isn't made after 30 days' notification.

Many CC & R's do not require approval before building. A lot depends on what town you are in, how "with it" the attorney who wrote the CC & Rs was, and when the subdivision was developed. In our smallish town many CC & Rs do not even require an HOA, let alone an Arch. Control Committee. And then there are those subdivisions which may technically require and Arch. Control Committee, but no one has stepped up to the plate to take the position on the Board of Directors and so no one is really overseeing the building going on.

But dockside is right -- if this is a problem, the CC&Rs need to be changed quickly. Easier said than done because normally this requires agreement amongst all the neighbors and notorized signatures. And, of course, after that, someone needs to be in charge of rule enforcement -- a real fun job!

In our town, they won't issue a building permit if the house doesn't meet the covenant specs. Same thing with a garage. They know which subdivisions have HOA's and covenants, and you have to provide an approval from the HOA's ARB before you will get your building permit.

Builders often leave themselves an out in the C&Rs to avoid having to deal with the HOA that they created.

They can delegate that exemption to other builders in many cases also.

You need to review the entire C&R and creation documents to see if anything is enforceable against the builder, his successors and assigns.

Seems sort of late now that the place is almost complete. Maybe you should go after the HOA for being asleep at the wheel