If your sink pop-up stopper will not pop up or seat correctly, fixing it is can just a matter of adjusting a few parts. The issue is often a clump of hair or other debris around the bottom of the stopper or the pivot rod. Also, the clevis may be out of alignment.
This is how to fix your Sink Pop-up Stopper issues:
1) Giving a slight twist, try to pull out the stopper. If it is bound to the mechanism, go under the sink and unscrew the pivot rod holding nut and pull out the pivot rod to separate it.
2) Pull the plug from the drain. Remove any hair and grime. If the stopper is broken or its seal looks damaged, buy a new one.
3) Lower the stopper back into the drain hole. Install the pivot rod as to engage the hole in the bottom of the stopper, and secure it on the retaining nut with the stopper in its upwards orientation.
4) Back off the set screw on the clevis, then, adjust the strap to a position to where it operates the pivot rod to open and close the stopper. Tighten the set screw and your done.