Hmm, particularly bad rules that ruin an otherwise great game...
Note that anything I say below is my opinion, and therefore more valid than anyone else's opinion. But I can usually provide references to people who are better at arguing than me.
Mutants and Masterminds is pretty awesome. But it does have a problem (besides the "Balance? What balance" inherent to class-less, which is at least puts a roof on with the "numbers are capped by power level", though other things can work around them). Toughness saves. I didn't like the idea that any attack could potentially take you out of the game, and a few play attempts confirmed that it was annoying.
I then realised "If you play this, you will max out your Toughness save with forcefields or whatever." That made it better, but meant you had to spend resources on it. I *then* realised that thanks to Invulnerable Toughness, designed to make you immune to mooks, you can seriously benefit more from having a bad Con score:
Toughness save can be no higher than Power Level + 5 (IIRC)
It is equal to Con mod + power bonuses
Therefore, if it's PL 10, and you have a Con of +5, you can have a total of "Protection 10". If it's Invulnerable Protection (it is), that means you ignore attacks with a strength of 10 or less.
So let's take a Con of -4. You can now buy a total of Protection 19 (19-4 = 10+5). Make that Invulnerable and suddenly, you're outright immune to any attack with a strength of 19 or less. Here's the kicker: no-one can actually have an attack strength of 19 or higher at PL 10.
So essentially, the mechanic as a whole was annoying, and their solution to it (everyone buys protection, and probably makes it invulnerable so that minions can't hurt them) created its own balance issues.
That's the best I can think of. I mean, BESM I loved, but that could barely be considered a coherent set of rules, I used to love Rifts despite there not being a single good (sensible, easy-to-understand, well-implemented etc.) rule in the whole lot. 3E has a lot of minor annoying rules, but nothing that would piss me off enough to set it all on fire and play "Fuck-off Edition". And most of those have been handled by Frank & K, anyway. As for "Fuck-off Edition", well, I consider it to be built out of pure unadulterated fail.
Oh, and White Wolf games also fall into the category of "Plenty of rules I hate. But they don't spoil an otherwise good game: it wasn't good to begin with."
I can't think of anything particularly rage-inspiring in Maid, Panty Explosion, CoC or SLA Industries, the other main systems I know about.