The gist of your story is that the house you purchased is larger than represented, both as to an office and as to the garage. The question is: how do these discrepencies damage you?

Is it something that you will need to disclose when you sell the house? If so, will that lower the sales price (causing you damage)? The larger question is why were you going over the plans in the first place? Are there other issues you are having with the construction? It will take more investigation into how your specific County may deal with these issues to really evaluate if these issues will cause you damage and, if so, what is the best approach for addressing such damage claims. I suggest you review this with an experienced attorney in this field.

The problem I see is that if the office was not approved by the building department, then it may have to get certified as to being up to code.

Ignore Ocean Beach. This is a zoning issue, not a building code issue.

To answer Mr. Feldman's question and yours, the possible damage to you is that this is an unapproved variance from the Santa Clara County "-n" zoning ordinance for unincorporated residential neighborhoods adjoining the City of Los Altos. Accordingly you a) would have to disclose this variance to prospective buyers, and b) if the county discovers the variance, THEORETICALLY you or a subsequent buyer may have to expend money obtaining permission for the non-conforming use. With that said, there are probably more non-conforming structures in the Bay Area than conforming ones, and your variance is pretty modest. If the county approved the larger garage, they would have trouble making an issue about it even though a formal variance was not obtained. So we're talking a 2.5% overage on the Floor-Area-Ratio. The County of Santa Clara doesn't have the time, money or personnel to chase down an unapproved 114 sq.ft. variance in a 4350 sq.ft. house. So if you don't raise the issue with them, the chances you will ever hear about it are very remote. Do be sure to disclose the variance on the seller's disclosures when you go to sell, however, or you may be liable for the failure to disclose.

If you really want to pick a fight about it, you probably have the right to have the builder/seller and maybe the architect go to the county and obtain a variance for you, or pay the expense of you doing it. That would be your measure of damages in a law suit. On the other hand, they would argue that your measure of damages is the reduced value of the home. Since the worst case scenario is the county finds the variance and demands that you obtain an approved variance or face demolition, and the likelyhood of that is very slim, most buyers would probably not pay a whole lot less for the house upon resale. So unless you have an attorneys fees clause in your purchase contract, you may spend more on attorneys fees than you would recover. The architect may have no liability for how their plans were used, unless the archictect was the one who obtained County approval.

Lastly, to answer your second question, the County has sovereign immunity from lawsuits having anything to do with approvals of plans or any other kind of design documents in connection with construction, including immunity from failure to properly inspect permitted work. So you have no recourse against the county, except perhaps a waiver argument if they ever actually tried to enforce the zoning.