Hello regina,
the manual tie points you placed are markers (with no reference location) and not automatic tie points. So they will appear in the markers section of WorkSpace and not affect number of automatic matches or tie points.. In example, images 5993 and 5994 were aligned placing 4 manual markers (points 1 to 4). As you can see there are no valid matches between the 2 photos...but 4 manual points or markers.