Yes, this is a known limitation.
For a tracker report, when you select more than one value from a multi-select, user-defined field as filter and if an artifact is associated with all of the selected values, then that artifact's record is duplicated for each of the selected values.
For example, assume that you have a 'Select User' multi-select, user-defined field with values 'User 1', 'User 2' and 'User 3' in a tracker report. All these three values are associated with 'artifact 1001'. Select all three values as filter and generate the tracker report. You will see 'artifact 1001' record being duplicated, that is, you will see three individual 'artifact 1001' records created for each of the three users.