First off, bureaucracy is not a "class," the Socialist states like the USSR were controlled by the Proletariat. The formation is described in Soviet Democracy by Pat Sloan, or you can check this infographic if you prefer:

Anyways, back to your question. In the instance of single-unit factory councils, it isn't so much as a "ruling class" as it is that these workers have control only within their immediate domain, and no real control outside of it. The Soviet model is different, it laddered upwards and extended equal ownership over all within it.

The Marxist critique of the cooperative model is that trade between these cooperatives will result in the resurgance of Capitalism, not the elimination of class society, as time goes on and some cooperatives swell in power and others fall under their control, without equal ownership between them. Engels elaborates on this in Anti-Dühring. Cooperatives don't scale without administration, either, which means at that point you may as well extend ownership equally across the whole economy so that it may be democratically controlled by all, even if those more local to an issue have more of a voice.

Now, that doesn't mean cooperatives are bad, it's just that they only really serve to play a role of "filling in the cracks" large industry leaves behind, as said large industry should be publicly owned. Cooperatives being small can remain as such, and only make themselves able to be properly folded into the public sector when they grow to include large networks of administration, at which point they have outscaled their original cooperative nature anyways.