Any unbalanced earthwork is apparent as soon as I run the cuts and fills. Some sites just can't be balanced because they are bordered by existing hard structure on 2,3 or 4 sides, and they are what they are. Plenty of other factors can come into play such as getting sewer and water to leave the site on their own accord, or entrance and exit slopes exceeding allowed grade percentages. If the engineer has a reason, fine. But if he doesn't have a reason, and the site's out of balance, by the end of the day, I'll make him looked like a smacked behind to whoever is paying him.
I've been doing it long enough that I can tell if the site is unbalanced because of the engineers ignorance or complacency, or even his unwillingness to change the design he's been working on for the last couple months. Thousands of dirt jobs give me the experience to look through the BS that contour lines portray.
If you are working the site and come to the stark realization that you're going to be short on dirt, that's your fault for not running the cuts and fills ( that's just generally speaking and not directed at the OP ). If it's the case where the owner or GC is providing quantities, I still always verify them, and if they are dictating quantities, they are most certainly responsible for any import or export required to bring the site into balance. ( and if that happens, they are at the mercy of my pencil ) And as far as topo being off, one of my first line items in an estimate is verification of existing topo. 6" low across the board on a 20 acre site can equal a lot of dollars.
I never go into a site without knowing my quantities and options before hand. I routinely bid sites with 100, 200, 300 thousand yards of dirt or more. And, there's just a host of things to do balance a site while it's being worked as well, especially a big site. Balancing a site by raising or lowering the site uniformly is child's play, raising and lowering specific areas within a site and making sure everything works is an art form.
But like you said, some engineers still don't have a clue, or just don't care. 20 years ago, it was out of hand, but most recently, most attempt to try to bring balance, but a lot of them do it on strictly surface to surface basis, and have no clue as to the importance layers and the manipulation of said layers can have on the overall dirt balance.
So, I feel your pain, and thanks for bringing up an interesting and important topic!