This helped a lot, thank you!
What I found out was that when I imported the .pdf file into SCALP3, it had turned both the "fill" and "stroke" of my design into cutting paths and separate layers. I fixed it by going back into my AI file and got rid of the "stroke" on my object (also works other way around by eliminating the "fill" instead). It then only created one cutting path and layer in SCALP3 when I imported my new .pdf file.
Thank you!!