When I have been able to index most of the peaks in a powder diffraction pattern, but there are remain a small number of unindexed peaks, I will immediately think that an impurity is present. However, one should also consider that these peaks arise from the presence of lowered symmetry that either removes a reflection extinction condition or expands the unit cell. There are two ways that one can look for this.
One way is to generate subgroups, using the “Run Subgroups” command in the “Cell Index/Refine” menu. This will generate a list of unit cells and space groups that can be considered, as was done with autoindexing results. This is described in more detail in §28.3.1.0.
The other approach is simply to look if doubling (or very rarely) tripling one or more unit cell lengths will index the previously unindexed lines. As has been discussed in §28.3.1.0, you can quickly expand a unit cell length(s) that are specified on the “Unit Cells List” data window by placing a 2* before or a *2 after and the value will be doubled. This will allow you to see quickly if an expanded lattice will index these extra lines. If so, looking more carefully at subgroups may then be helpful.