I've seen reference patterns misbehave in the past for a variety of reasons (multiple patterned references for example) but this seems like a bug.
The 1st part has a pattern of holes.
The second part is assembled using one of the holes.
The third part (the screw) is assembled using a mate with part #2 and an insert to part #1.
The selected part #3 for patterning. Reference type is an option and when selected the hole patterned in part #1 is correctly location hi-lighted with member dots.
Accept/Done and the model tree shows the correct number of members but they are all in hole location #1. Reversing the order of the assembly constraints corrects the members final placement.
Remember, there is only one pattern to be referenced and the software correctly identifies it during pattern definition but incorrectly executes it in final placement.
Is this "intended functionality"? I hope not.
Rant over ...
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