Some of the balance issues in the game aren't really the major, obvious ones like...tric mines, SNB DOFFs, and so on. Those are problems of course, being the huge, 'here I am, look at me!' ones, but not always.
Honestly, something that tends to make something unbalanced is more the fact that it's the unintended side effects or such.
Take the Cryo Pulsewave. Introduced as part of the reward on Nukara, right? Pretty simple, meant to be used against the Tholians. What ended up happening is that the cold damage is does, has NO resistance given in any armor except EV suits (which just makes you more weak against other things at that point), so it was, and still is used VERY often to immense effect on one-shotting people with things like Ambush, Stealth Module, etc etc.
SNB DOFFs are in a similar lane, just from a different reason. Awhile back, SNB DOFFs were rare, very rare, and...*in Mr. Dink's voice* VERY expensive. They were seen only once in awhile, maybe one per ship. Extremely powerful, absolutely, OP, sure, but not to the insane degree we've eventually seen now.
But for a week, the old lockboxes dropped, along with some updates to them, including making Cardassian lockboxes potentially drop a rare single DOFF pack, which when opened, could potentially hold an SNB DOFF. So all of a sudden and outta the blue, these things dropped considerably in price, and well...you all know the rest of that story.
Those are just two examples, I am sure there are plenty more on top of that. But yeah, just seems like a good part of the time, the balance issue comes not so much from the things they release, but the unintended things they cause, like a combination of items and/or abilities they probably didn't think about happening.
I'm sure this is something most of ya'll knew of a long time ago, but I thought I would talk about it, since I'd been thinking about it earlier.