Unfortunately at this stage you can’t manually rearrange the images in a shape collage. What you can do is to click the Shuffle icon (the first icon in the set along the top right of the photo) to do a random rearrangement. You can keep clicking this until you are happy.
The other thing you can do is reduce the number of photos in the collage to the exact number of images you’re using. This can be done using the “Number of Photos” slider in the left options bar. So if you make it 60, there shouldn’t be any duplication.
When you open a Shape Collage from the PHOTOS > History tab, to get back into the collage-builder mode (where you have the option to shuffle), you simply have to “Undo” (the icon is to the top right of your image) until the option appears.