There are many examples where self-determination means secession of a territory from a state, typically opposed by the latter. The most obvious recent example are the eastern regions of the Ukraine, but one could cite many other examples:

• In the cases of South Ossetia and Abkhazia, Turkish and Iraqi Kurds, and Catalonia the secession is opposed (or, at least, not encouraged) by most western powers.
• The most recent case of widely recognized independence is that of South Sudan, but also that of Israel or the Palestinian people (the latter is not a de facto independence, but widely supported throughout the world). The breakup of Yugoslavia provides an extreme example, where several parts of this country seceded from it one after another, with different degree of western support.
• There are also ambiguous cases of de facto independence, not acknowledged for political reasons, e.g., Taiwan, Hong Kong, or the cases where the international community is ambivalent - e.g., independence of Scotland before and after the Brexit vote.

Wikipedia article on self-independence contains a list of other notable cases.

Obviously, whether a nation is recognized independent or not is eventually determined by whether this independence is acknowledge by most of the international community or, at leats, by its more influential members. The question is therefore somewhat abstract:

Is there a clear legal basis (in international law) for distinguishing the cases of legitimate quest for self-independence vs. the illegal violations of territoral integrity or is upholding one or the other merely a matter of political expediency?

A related question:
United Nations : Right to Self Determination and Secession working groups?