I have had this occur on a few occasions, but (as I have a minor issue in my PC) I thought nothing of it (as I felt it was related to my PC, and I am going to re-work it soon). However, now I know it is also affecting other Players I will document what I have found about this problem so far.
The problems only occurs when there are Secondary Stars, and one (or more) of these Secondary Stars have objects orbiting them. These Secondary Star systems are not part of the Primary Star system objects (I have had occasions where a Primary Star has had a Brown Dwarf Star in its' group, with objects of its' own, and been able to scan ALL objects within the Primary Star group without the problem occurring).
The Primary Star does NOT need to have objects (other than those relating to Secondary Stars) orbiting it.
The objects orbiting the Secondary Star need to be close enough (in relationship to the position of the scanning vessel) so that the FSS would need to zoom in more than once (I have had a Secondary Star system close enough that I was able to scan all but two objects without having to move from the exit point of the Jump. The further away the Secondary Star system is the more likely the problem will occur.
Once I have got close enough to the Secondary Star system I will be able to scan the objects within. However, if there are still some objects that cannot be separated without zooming in further the problem will occur again, so I will need to get closer to the Secondary System.