PDF opens in duplicate

I am opening pdf's into illustrator to amend and save as AI files.
They open as grey scale shapes which is fine, I then change the grey area fills to hatching then save as AI files.
PROBLEM: Each PDF drawing opens in duplicate or triplicate on the same layer. I then have to go through each drawing deleting the shapes untill I end up with one instance of the drawing that I then edit.
Fo example: I have a grey circle within the drawing which I want to change to hatching within the circle. I do this but there are 2-3 identical circles on top that I have to delete first.
Is there a function that will combine the layers into one, within the same layer.
Thanks

Anybody?

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