Adventure games that force you to solve a puzzle by some single incomprehensible string of bizarre moon logic, when there are clearly several more reasonable/practical/possible options present.
Screw-you-missions: Where you're originally sent to accomplish objective A, and immediately afterward have to accomplish B or fail - B, of course, will cause you to fail at least once since you don't expect it. Ie. in the Rising Sun campaign of RA3, you have to destroy a huge base mainly with a single super unit. Roughly ten seconds afterward, you'll have to shoot down an aerial unit within 15 seconds or fail the mission. The super unit has no AA capabilities.
Badly made alignment-related choices. Ie. in most Bioware games you pretty much have to be either Retarded Evil or Nutless Good - the games actually to tend to punish you for being anything in between, provided you get the choice in the first place. This is especially jarring in D&D-based games, where there are usually NINE aligment options in total - yet the games keep pushing the player towards either Lawful Good or Chaotic Evil, even when it makes no sense to do so.
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