Fan-Preferred Couple: Most likely unintentional, but every one of Obsidian's titles where romances are present almost invariably results in the fans embracing a character who is not available. Knights Of The Old Republic II has Bao-Dur and Mira, Neverwinter Nights 2 has Neeshka and Sand, and Alpha Protocol has Sis. It's worth noting that different fans may prefer a non-canon romance in one game while preferring a canonical one in another.
When developing Knights of the Old Republic II: The Sith Lords, LucasArts told them that they were going to delay the release until a bit into 2005 (Some speculate Lucasarts were hoping to cash in on the renewed interest in the franchise thanks to Revenge of the Sith). Obsidian decided to use the extra time to expand on the game, before LucasArts suddenly decided to revert back to the original Christmas 2004 release date. Since the delay at this point had been a spoken agreement and not a signed contract yet, Obisidian had no choice but to rush the game out of the gate, meaning that several quests and mechanics, including much of the ending sequence, were left incomplete or broken. And when Obsidian offered to put out a free patch fixing most of these issues, LucasArts denied them permission to do it, leaving the fans to try and pick up the pieces with mods. The point may have been academic; the game sold most of its copies on the Xbox, and wasn't enabled for Xbox Live, meaning it couldn't be patched.
When Alpha Protocol was nearing completion, SEGA said they weren't too happy with the current state of the game, and announced they would push the release date back a couple of months. Obsidian hoped that this would leave them with more time to give the game some much needed polish, the logical thing to assume since the game was delayed anyway, but when they appealed to SEGA for more development time in the delay period, SEGA flat out refused to greenlight it.
During the development of Neverwinter Nights 2, Atari demanded that the game have a Christmas release, forcing Obsidian to rush to a finish, cutting out a lot of characterization for your party members and two romance arcs in the process. The worst part, though, was that they hadn't finished working all the kinks out, so when the game was released it was horribly buggy and hindered by bad gameplay. Later patches fixed that problem, but the fandom was left seething for a long time.
Later, when the game first and only DLC, Mysteries of Westgate, was under development, Atari demanded that would ship with a DRM scheme. This caused the adventure pack to be delayed almost two years, causing an uproar in the fanbase. By the time it finally came out people had mostly lost interest. A few months later, Atari took the DRM off the game, expansions, and Mysteries.
And, of course, there's the infamous "New Vegas got an 84 on Metacritic, so no bonuses for you" incident, which almost killed Obsidian outright and actually led to a lot of accusations of skulduggery on Bethesda's part from the fanbase. Notably, quite a few reviews took a couple points off the game's score because of bugs, and Bethesda was responsible for the QA on the game; meaning if Bethesda had done their job properly, Obsidian wouldn't have been tossed into dire financial straits. Some of the more malicious tongues claims that Bethesda did a bad job on purpose to avoid having to pay Obsidian a bonus, but Obsidian themselves has denied this to be the case, and most people point to Hanlon's Razor, noting that Bethesda's QA work always has been infamously lacking.
South Park: The Stick of Truth is an odd case: it got screwed by the "network" imploding like a black hole. THQ went under completely and the project had to be picked up by an entirely new publisher before it got out the door. Frankly it's impressive the game got out the door at all, considering.
All this is what eventually spurred the development of Pillars of Eternity, a property owned and produced by Obsidian and with all profits going straight back to them. It gives them a much more stable financial base from which to produce their licensed efforts.