Complications arise when things aren't going well in the marriage, or the couple gets late in filing the petition, or both. Over the years USCIS has come out with several policy memorandums instructing officers on what to do with cases that aren't so clean.
Happily, I-751 procedure keeps being improved and makes more and more sense and it easier to deal with. It's always been the law that if an I-751 is filed late, it must be filed with an explanation. If that explanation was missing, under older law the I-751 would be denied. Or perhaps rejected. Under a new I-751 memorandum that was just issued in January 2013, the officer can simply request the explanation separately by issuing a Request for Evidence (RFE). A much more preferable option than losing the filing fees are perhaps finding yourself in removal proceedings. Or having your case rejected and having to refile it after your green card has already expired.
Confusion also arises when the marriage is not doing so well. If a divorce is imminent - but has not been filed, or has been filed but the hearing is months away - it is best to run your situation by a knowledgable lawyer. Chances are he's seen your situation before. And the consequences for not filing on time are pretty severe. Risking denial of an I-751 basically means you're betting on getting put into removal proceedings. It's hard for a lot of conditional permanent residents (CPR's) to accept, because their cases are so "clean" (to them) they do not appreciate that USCIS must put them in removal proceedings if their I-751 is denied, even on a technicality.
As far as what a good reason is to not file an I-751: In practice, USCIS does not make the burden onerous. Frequently some relatively minor issue comes up, distracts the party, and before they know it, the green card has expired. Our job as lawyers is to probe, probe, and probe to find the reason(s) the case was not filed on time.
But an ounce of prevention is worth a pound of cure. Take your I-751 obligations seriously. Be picky about the evidence you choose. Choose good evidence: nothing too weird or off-base. And use a lawyer. If you're filing an I-751 you already have a lengthy immigration history in the US. File wisely.