By clunky controls I mean opposite of fluid controls. There are different things in games which make the controls feel clunky, sometimes there is a latency or delay in the player pressing the button and the character in the game performing the action or not being able to press the right sequence of buttons in the right amount of time which leads to unexpected behavior of the character in the game. Usually when segueing from one animation to another there will be a stutter or an awkward lack of control while the system runs the next animation.
In short if the controls don't feel responsive or if it doesn't feel like second nature then YES! the game suffers with clunky controls. Players might get used to it and learn to play with it but it is a bad design and should be avoided.
1) Dark Souls
The largest contributor to that 'clunky' feeling is delay or unexpected behavior. Jumping in Dark Souls (first game) is clunky. That doesn't mean you can't get good at it, but the method to jump can be tricky and a bad jump usually means death. To jump, you double tap the dodge roll button, which is also the Run button. A lot of players who play Dark Souls for the first time think the controls are clunky in general. There are delays to swinging your weapon and commands are somewhat queued, resulting in unintended actions if you mash the button.
Also jump attacks and kicks/guard breaks are also pretty bad as the command is forward+attack which is really finicky. If the game decides that you didn't do it correctly you perform a standard attack and often leave yourself wide open to the enemy.