In this case the U.S. and EU have plumped for territorial integrity over self-determination, and the particular circumstances, i.e. the Russian invasion that preceded the referendum, have allowed them to claim the legal and moral high ground in doing so. But in the past the U.S. and many of its allies have occasionally made the opposite choice, recognizing states that have resulted from the breakup of existing ones (e.g., Eritrea, Bosnia, Kosovo), and while it is possible to paint some of this as simple acquiescence to faits accomplis it would be difficult to maintain that a wholly consistent, high-minded, and principled stance has guided all such past decisions.
Indeed, it would be surprising to find complete consistency in anything having to do with state behavior, since it is a truism that the world is complicated and that states navigate it by a messy mixture of interest, calculation, and principle, a mixture that is unlikely to yield completely consistent results. Scholars may try to discern a consistent thread that determines, for example, when the U.S. recognizes secessionist movements and when it does not (see, e.g., Jonathan Paquin, A Stability-Seeking Power, 2010; link), but without casting aspersions on the particular book just mentioned I think it would be wise to retain some skepticism about whether these often tangled situations can be tamed by a nice theory.
The problem is not only that states are guided by a mixture of considerations but that principles themselves, as mentioned at the beginning of this post, come into conflict. In an article published almost twenty years ago ("The Crisis of Liberal Internationalism," Foreign Policy, Spring 1995; link to pdf), Stanley Hoffmann put the point this way:
It is precisely in the realm of chaos I described above -- the realm of disintegrating states -- that the clash of norms is the most evident and paralyzing: Sovereignty (as a principle of order and, still, a barrier against aggressive or imperial designs), self-government or democracy, national self-determination (with all its ambiguities and flaws), and human rights (which are not devoid of ambiguities of their own...) are four norms in conflict.... Human rights...often cannot be protected without infringing upon another state's sovereignty, or without circumscribing the potential for a "tyranny of the majority" entailed by national self-determination and by Jacobin versions of democracy. The trouble-making potential of self-determination, both for interstate order and for human rights, is not so obvious that many liberals want to curb it or even get rid of it, yet the demand for it simply cannot be ignored, and denying its legitimacy would rarely be a recipe for order or democracy. Inconsistency is the result of this confusion: the international "community" has recognized Croatia, Bosnia, and Eritrea, but not Biafra, Chechnya, or the right of the Kurds and Tibetans to states of their own.Scholars emerging from graduate school with PhDs in political science or international relations are unlikely, I would guess, to find jobs these days if their work prominently features words like "inconsistency" and "confusion." The field tends to value work that purports to bring theoretical order out of apparent chaos. But confusion and inconsistency are often pervasive in the real world of international relations, and although "it's confusing" will not cut it if one is writing a dissertation, for those whose priority is understanding the real world "it's confusing" is not a bad place to start -- and, sometimes, it's also not a bad place to end up.