The problem is defining what "nation" is. Are Bretons a nation, or are they a part of the French nation? Are Catalonians a nation, or are they the part of a Spanish nation? Some answers to those questions lead to contradictions, in a sense that both groups adopt your "nation should be ruled from its own land by its own people" formula, but lay claim to the same land and/or people.
I admit the definition of a nation can be a bit vague sometimes, however, the examples you gave are quite straightforward and I see no problem whatsoever. A Breton nationalist wants Brittany to be ruled by Bretons from Brittany rather than by the French from Paris. A Catalan nationalist wants Catalonia to be ruled by Catalans from Barcelona rather than by Castilians from Madrid.
Who decides what a nation is can be a bit tricky from time to time. Who do NOT decide is much easier to answer. In both of your examples, it is clear without a doubt that the people who inhabit the said geographical regions are the ones to decide. Not the Frenchmen from Paris or the Castiians from Madrid.
If the people of Brittany decides that they want Brittany to remain as part of France then it simply means that they do not support Breton nationalism. From a nationalist moral point of view, it is up to the people of Brittany to decide. If a French nationalist wants to keep Brittany as part of France against their will then someone must tell that "nationalist" that he is practicing imperialism rather than nationalism. If a Breton "nationalist" wants to annex all of France to bring it under Breton rule then he is an imperialist rather than a nationalist.
Then it's solved like any political issue. Democratic elections seem to be pretty popular these days. Not a perfect system of course but many consider it better than the other alternatives.
