Marker detection is a great feature, but it can often be a hit or miss. One has to be very careful when it comes to size (which needs to be adjusted to the GSD) and shape/colour of markers that are used.
It would be great to have a more powerful marker detection where PhotoScan is first 'trained' with a picture of a marker that was used (any shape/colour) and then uses some computer vision algorithm (such as ORB) to find, identify and mark them in all images.
Regards
SAV