You're going to be held liable if you sign-off to something you know is non-compliant.Leaving the job open can create issues with further permitting down the line (sometimes the DOB won't issue new permits when there's an open plumbing permit in a building, but a good expediter can get around that) but the burden of completing the job in accordance with the plans is on the contractor (so fuck him). You're there to prevent him/her from completing a job that does not meet the standards set forth in the drawings.

I document everything before sign-offs.

I've had contractors demolish multiple partitions just because they thought they could get away with it (I'm pretty lenient about non-code-related items), even when I knew they'd rebuild them after sign-off.

Is it safe to assume that you've already pointed out the non-compliance to the contractor, and they've refused to correct it?

Is it also safe to assume that you've pointed out the non-compliance to the owner, you've rejected the work, you've refused to certify pay apps for the non-complying work, the owner has withheld payment from the contractor, and the contractor has continued to refuse to correct it?

In the real world there is almost no such thing as a "small"  ADA non-compliance if somebody wants to make an issue of it.  If the contractor fucked up, make him fix it.  End of discussion.  Don't expose yourself to unnecessary liability.

as long as you notify everyone in writing and in a timely fashion you will not be liable for anything. if you saw this condition mid construction and decided at the end to note it the client could have their lawyer indicate your negligence of a timely denial of construction and whatever costs incur by not being timely you will be pssibly asked to pay those losses/expeditures....... for the most part, depending on the building, and if no one ever goes for a new CO and the tenant when selling doesnt need a sign off to sell - frankly, it doesnt matter. i would wager 50% of all jobs never get signed off in NYC, maybe its down to 25% now... and in 15 years when its a problem your client will call me and we will clean it up etc...our fee will be more than your fee. god bless NYC!

^ But most building codes, including NYC, have adopted ADA's provisions and guidelines into the code itself.

b3ta, you're right, but it still might be a code issue. It really depends on whether it is a non-compliance with the ADA (DOJ wheelhouse) or if it is a ICC A117.1 issue (building code issue; see Chapter 11). I know you probably know this, but "ADA" is often used incorrectly as a catch-all term to indicate accessibility requirements/guidelines. 

There is also the issue the OP brings up with submitting record documents that either correctly indicate the non-compliance (which they don't feel would pass final approval), or show the as-designed condition (but isn't an accurate record document and the OP feels they wouldn't be able to ethically sign off). In that case, it probably doesn't matter whether it is an ADA or ICC A117.1 issue because either way would require the OP to sign off on record documents they either know are inaccurate, or non-complying.

nyc adapts it in and modifies it and has got in trouble as well for its modifications (in the past)

clarification for non NYC archs - the OP is most like doing a Directive 14 (1975) sign-off which means unlike other towns and cities the OP takes ALL responsibilty for accuracy of construction in accordance with approved drawings, there is NO dept. of buildings inspection. an inspector like the architect might give lee way to things like a door swing etc....its at their discretion essentially. in General ADA in NYC can get murky with apartments and the term "adaptable" is used quite often.

Is the project self-certified?

if self-cert and dir. 14 - straight to audit.