Take I Want to Be the Guy, for example. It's intended to be a loving tribute to old NES games while simultaneously being the most unfair game ever devised. This is a fine goal: it creates a unique and peculiar feel for the game encouraging paranoia as everything in the game is out to get you. If it was just the game elements I wouldn't have a problem but when your character stands on a platform moving down the jump button becomes unresponsive to about fifty percent of the presses. Needless to say the game relies on split second jump timing and a frustration is introduced before the player gets too far into the game that is completely unnecessary.Without seeing the code I'd say that there is simply a timing disconnect between when the game checks for keypresses and when it moves sprites (moving objects on the screen). So sometimes the platform moves, then it tests the jump button condition and finds the character is not standing on anything, and then the player character falls to catch up to the platform where another test occurs. I haven't dealt with this in Flash but the simple solution would be to expand the "standing" check for the jumps to allow for that one pixel difference between the player and the platform.
And then there's Dwarf Fortress. A game with an interface that was congealed rather than designed. For all the cleverness in design and behavior contained in the game the vast majority of people who look at because of the recommendations of other players can't even get started with it. The interface has no less than four completely different ways to select an area and chooses between them at random. Each menu has its own unique method of selecting something. Status and feedback on the player's choices is often deeply buried. There's never less than two different ways to do everything and which one works and which one does something completely different for just that section seems to be random. Dwarf Fortress is a perfect example of how to try to kill a good game concept with a bad interface.
I know to some extent it's a case of getting what you pay for but I'm starting from the possibly foolish assumption that the people who made these games want as many people as possible to play them. Interface design isn't as cool as adding a new boss, lightning effects, or special monsters but it is what the player is really going to be dealing with the majority of the time and doing it poorly hurts you. So please, amateur game designers, put at least some effort in it.