To solve the problem, you will need to place an aperture with centroid enabled on the brighter star (i.e. the usual way to place an aperture, it will show a "+" sign in the middle of the aperture indicating centroid is enabled). Then place another aperture
on the faint star, but disable centroid first by clicking the centroid icon () above the image display (these apertures are just a circle with no "+" sign in the middle). After clicking the centroid
icon, its background should show light gray rather than dark gray indicating it is disabled. You may even need to offset the aperture on the faint star to exclude as much of the bright star as you can to improve the photometry of the faint star (but you still
need to include most of the flux of the faint star in the aperture).
If you need to place additional centroided apertures, you should click the centroid icon again to enable the centroid feature before placing the additional apertures.
Even though centroid is disabled for one or more apertures, as long as one or more other apertures has centroid enabled, the non-centroided apertures will follow the average movement of the centroided apertures from one image to the next. So, even if your
tracking/guiding is not perfect, the non-centroided apertures will follow the image shift detected by the other centroided apertures.