Yep. Specifically, you had the changeling Admiral Leyton who quite easily engaged in a thorough planet wide military takeover while the feckless President Jaresh Inyo was wringing his hands in his comfy office in Paris, watching the rest of the world burn from Red Squad attacks.Which is really not a very accurate depiction of things; especially on DS9, we saw Starfleet officers in the field making decisions that really should have been made by the democratically-elected civilian government, not a captain on the front lines. Star Trek really ought to feature the Federation President and Council more than it does.
Kind of shows how scary-weak Federation leadership was, relying more on the perceived strength of the historical concept of the Federation as an abstract, rather than the ruling class making any kind of substantive decisions.
Starfleet, and to some degree Section 31, were the ones really running the show.