I'm old enough to recall the last Congress of the Yugoslav League of Communists (SKJ), in January 1990. After their demands (to scrap the unified Party structure in favor of more power to the republics) were rejected, the Slovenian delegation walked out. The Croatian delegation joined them. Thus began the collapse of Yugoslavia.
In Slovenia, the Communists re-branded themselves as democrats; the first "democratic" president was the very same Milan Kucan who led the Communist walkout. His Croat colleague, Ivica Racan, was less lucky; he would play second fiddle in Croatia's independence drive to chauvinist Franjo Tudjman. But throughout 1991, Slovenia and Croatia were allies in the fight to assert independence and dismantle Yugoslavia.
So I have to admit a certain sense of schadenfreude when I read about the ongoing border feud between Slovenia and Croatia, which is interfering with Croatia's bid to join the EUSSR. Having disposed of Yugoslavia and either "erased" (Slovenia) or ethnically cleansed (Croatia) their unwanted inhabitants, Zagreb and Ljubljana are now tearing at each other with hatred previously reserved only for the Serbs.
The heart of the dispute is Croatia's assertion of maritime borders that would deny Slovenia access to the open sea in the Bay of Piran. On one hand, it is hard to be sympathetic to Zagreb; Croatia already controls most of the eastern Adriatic, from Istria to Dubrovnik, some 1000km of coastline. Slovenia has about 50km, Bosnia has less (and even that on paper only), and Montenegro has the rest. On the other hand, Slovenia is clearly using its position of EU membership to strong-arm Croatia on the issue.
Not surprisingly, the commissars in Brussels see the entire affair as horribly embarrassing. Not only does it interfere with their plans to annex Croatia, it undermines the whole 1990s narrative of "democratic" Croats and Slovenes fighting together against the evil Serbs.
Personally, I think Slovenia is doing the Croats a favor, albeit unwittingly. If they thought Yugoslavia was "violating their rights," wait till they get a taste of the EUSSR! At least the Croats had a fair bit of power and influence in Belgrade, making the break from Yugoslavia that much easier; breaking away from Brussels will be quite different. And given the whole animosity for the Slovenians, which appears to be mutual, one wonders why they'd want to be in the same polity with each other again. Ah, but logic and EUSSR seldom mix.
Croatia and Slovenia became bedfellows in order to kill off Yugoslavia (which benefited them both enormously, by the way). That marriage of convenience is long over. Yet I find it hard to feel sorry for either.
You wanted "independence"? There you go. Have fun.