SNIPPED for length
Spells vs Skills
The same PC abused Greater Invisibility. That spell as written is broken. It's effectively giving you a +20 to Stealth, in a game where most skills do not automatically increase with level. My own druid would have difficulty spotting an invisible creature (at level 7, the minimum level to cast that spell, my druid would have Perception +13, from training as a class skill with levels and Wisdom) against a typical DC of 22 or so (wizards tend to have a little Dex). At minimum that spell should have a scaling Stealth bonus, starting a lot lower, or emulate the 4e "Hide in Plain Sight" mechanic instead. It's actually worse in Pathfinder than in 3e because the bonus is to Stealth, not just Hide, so you can't use your sharp hearing to locate them ... oddly enough.
A spell used by our witch when they joined the party. It's 3rd-level and covers a 40 foot radius cylinder. What is so broken about it? We once got in a fight with a bunch of barbarians. They had decent Dex scores but no ranks in Acrobatics. They had about +2 total to Acrobatics, despite high levels, because of the way skills work. The barbarians were lucky to make their checks and move at half speed, while our magus blasted them with Lightning Bolt. (They were also hemmed in by my druid's Spike Stones, which don't deal that much damage but cripples their movement even further, plus the Perception DCs are obnoxiously high.) Most spells that force skill checks aren't balanced in Pathfinder. The Create Pit line of spells is a great example. The good news is this is fixable... with house rules.
Random Nuttiness
We twice ran into really unfair swarm monsters. The first time the monster was a swarm of bats, which consisted of Fine creatures, so was literally immune to weapon damage. We ran into them in a tomb, and being only 3rd-level (without our wizard, who had left) that we had literally no AoE spells. We had to leave, and my druid prepped a Gust of Wind to deal with the situation the next day. That actual plot-relevant villains were easier to handle.
The second time, with a few more levels under our belt, we ran into swarms of ravens, which could pluck out your eyes as a standard action, at will, and of course this is permanent blindness. Half the party ended up blind. Worse, we didn't have a cleric, only a druid and oracle. Druids don't have Remove Blindness as a spell, and oracle spell lists are very limited. If your oracle doesn't have Remove Blindness as a known spell, then you're in trouble. Trudging to a town to get some potions was painful, and the DM didn't throw any encounters at us during that time period. Once again, the plot-relevant villains were not nearly so hard to deal with.
Long-term crippling effects suck. Also oracles just aren't as good as clerics, leaving me a little mystified about their popularity. (The oracle had the curse that prevented you from speaking in combat. No quips, no tactical discussions, no taunting, no warnings, nothing.)