Flawed protagonist

Examples:
* Has serious anger issues, lashing out at people who mean no ill to them.
* Character is exceptionally selfish to a point they sabotage others just to get what they want.
* Unable to accept personal failures, thus deluding themselves everything's everyone else's fault.
* Refuses to accept facts when they don't align with their own beliefs.

Some of these are traits of "evil" characters, but not really malevolent characters, since the damage done to others is not done out of illwill towards them, but rather some other reason.

Related:
* Tragedy

Most commonly video games have characters without any significant flaws in character (infallible). They may bicker, have biased views, fears, etc. but essentially this never is a problem.

NOT for cases where the flaw is minor and only serves to make the character more life-like but otherwise has no or little impact on anything.
NOT for cases where the flaw is removed or temporarily avoided.
NOT for physical flaws.

Being evil should NOT be considered a flaw. Thus malevolent, and by extension antihero protagonists, should not generally be included unless the flaw is somehow exceptional.

Amnesia shouldn't generally be considered a flaw, but may be if it does function as a flaw more than as a way to introduce the player to the new unknown world.