Couple of things that have happened in games I've played in:
Background: The early days of D&D 3.0. Splatbooks weren't even published yet. We're 16th level and feeling all big and bad. We decide to go attack the red dragon that was attacking the area.
Problem: The DM was used to running 2nd edition, wherein the dragons were pushovers. He bumps it up an age category, gives the dragon max HP, some really useful magic items in its hoard (which it was wearing), and two of the spells it can cast: Heal and Haste (both extremely more useful in 3.0 than 3.5). He lined its lair with traps. All pretty much standard for him when running dragons that are meant to be a tough (but not impossible) fight. He didn't even think twice about it, and didn't up the CR accordingly.
Result: TPK, and the loss of two players (they quit the group because of that session).
Background: D&D 3.0. The party needs to get to X location in a homebrew, half-way across the continent. We decide to sign up with a caravan traveling there.
Problem: The DM decides that, even though we are on a major caravan route, we have one fight every other day or so. However, he didn't take into account the fact that because of the number of PCs and NPCs, you got one fight and maybe a little roleplaying in each session. Since we played twice a week, that equaled out to 6 months real time.
Result: Major player boredom, as the players did nothing but roll dice all session for three months real time, at which time the game finally folded (see below).
Background: Same game and caravan as the last example.
Problem: An NPC caravan guard attacks the caravan master in the middle of the night. PCs discover this and prevent him from killing the caravan master. NPC uses
Fly spell as a method of escape. DM had planned for this, since he knew we didn't have means of flying as fast as the spell, and our horses couldn't go that fast. the NPC was supposed to turn into a reoccuring villian.
Result: DM didn't take into account one of the characters who was a Ranger were-cheetah (from a non-WOTC source). She had the appropriate feats (Run, Endurance, etc) to follow him, speed-wise, on the ground until the spell duration expired. She also had a Bounty-Hunter PrC that allowed her to follow/track anyone in just about any circumstances. She stated she followed him (shocked look on DM's face). So, her PC followed him for a while, then lost sight of him when he flew over a small forest. And she couldn't find him even though there was nowhere he could have gone. That was the last game session we played in that campaign.
Background: This one features me as DM. D&D 3.5 homebrew.
Problem: The party is getting bored because we have several sessions since the start of the campaign and no fight yet - nothing but in-town RPing. I don't quite realize this yet and prepare the plot hook. I send an NPC into the tavern where the party is to give some information that the party needs. The barkeep, who is known to the characters, sees the NPC and pulls out his weapon for protection, because the NPC is the henchman of someone that the barkeep knows.
Result: The PCs overreact and the players gleefully attack the NPC, whom I did not have statted out.

I had to wing the whole battle, making not much of a challenge, though I tried.