The pop-up stopper mechanism can become dislodged over time, causing it to sit crookedly inside the sink drain. Normally all this requires is tinkering around with a few of the parts underneath the sink. To get a good idea of the situation you should ideally just remove the pop-up stopper and go from there.
Lift up and turn lightly on the pop-up stopper to see if you can simply just lift the pop-up stopper right out of the sink. Some pop-up stoppers can be removed this way. If you cannot remove the stopper this way, you will have to go underneath the sink to remove the stopper.
Find the stopper's tail pipe sticking down underneath the sink cabinet. The tail pipe is easy to spot as it is the long, straight piece hanging down from the sink bowl.
Reach your hand in and find the sink stopper nut fastened on the back of the tail pipe.
Undo the sink stopper nut from the back of the tail pipe. This allows you to remove the sink stopper control rod, also known as the pivot rod.
Remove the control or pivot rod. You will now be able to remove the pop-up stopper from the top of the sink.