There was a pretty good two-parter on DS9 where an admiral took advantage of the fear around the dominion war to over-step his bounds and implement secretive/dr

There was a pretty good two-parter on DS9 where an admiral took advantage of the fear around the dominion war to over-step his bounds and implement secretive/draconian security measures until Sisko "blows the whistle." Probably came as close as any episode to showing Starfleet dysfunction. And of course there was Section 31 towards the end of the series (starfleet's NSA). There were also a couple TNG episodes: one where there was a witch hunt to find a supposed spy on board the Enterprise, and another where Starfleet claimed Data was property and not alive. There's also Star Trek 6 which exposed a Federation conspiracy to sabotage peace talks with the Klingons. Probably my favorite movie in the series after Khan. Granted it's much earlier in the Trek universe, but Enterprise also tackled xenophobic groups in the last season. I always enjoyed episodes that featured internal struggles even if they were relatively rare.