I figured out the problem. It was an index I created outside of my schema. The index is meant to create a lot of substrings for a text based search. My script added the index every time before I uploaded the documents. So even when I deleted it from Fauna, the index would always be recreated before I did a document upload.
However, this does pose an even more interesting dilemma. Because of the ability for this index to grow in size considerably, does this mean that I would not be able to upload more documents to this collection in the future because of how this index is constructed?