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* just because XDS decides not to use some spots for indexing doesn't mean these initially non-indexed spots really belong to a separate lattice: compare the indexing/orientation matrices for the different solutions to see if they are significantly different (e.g. related by a one degree rotation). Also, check your images visually (ideally with the predictions on top) to make sure you acrtually have several lattices.
* the refinement of parameters (during the INTEGRATE step) can be very unstable: often, the spots of the two (or more) lattices are very close together: during data collection, some orientations of the spindle axis might make them move even closer until full overlap. At that point (or shortly after) the parameter refinement might 'jump' into the wrong lattice by chance. So look out for any jumps in parameters (distance, detector origina, scale, mosaicity etc).