In all the per site meta, on the Activity tab - REPUTATION section, the reputation score is displayed with the background color: #eff0f1. So looks like the "top n% period" link is (200+ reputation sites only) displaying without the proper margin.

When inspect the element of the div, CSS class bg-black-050 contains the background color, that caused the display issue. The same class is not applied in the main sites.

Can be the bg-black-050 removed from the reputation DIV, or the "top n% period" added with proper margin?

Screenshot from Meta Stack Overflow: