Your .mp4 files must be spanned.
Ie, when you shoot continuously, XDCAM EX will create multiple .mp4 files and create references between them. So a single shot might have files A, B, C, & D, but they're effectively one master clip. (P2 works in the same manner, btw.)
By importing the parent folder, you've asked Premiere to import clips A through D, but Premiere is recognizing that they're all one master clip, & stitches them together. So you end up with 4 copies of each. Mildly annoying, but better than having to stitch together the pieces yourself manually.
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