I wanted to rule out this being a feature of org-capture, maybe a result of manually editing the file or something?
If anyone has any other suggestions as to what else could have caused it I would be very appreciative.
The org-capture template was just an empty todo bullet under a heading, I added some bullets which were not TODO's to the end of the file recently. I don't know when exactly the file rename occured.
Edit: I should clarify that upon creating a new capture it created a new file filename.org. No new captures are stored in filename (1).org