...Why am I getting these duplicates?
Sounds like a LR issue, perhaps caused by you using LR Import to
1) copy image files to final destination (location) on disk
2) register (new) images in LR's database
That is what you would do if LR imports from a memory card. If you use LR import to register image files that are already at their final location, I believe you want LR Import to skip step 1.