After an hour or so of trouble shooting, the answer is fairly simple, although I am not entirely sure why it works.
what i did was create a text file instead of a csv file which I was doing in my original question
with open(FILELOCATION + utcnow.strftime("%Y-%m-%d") + "-" +site+"-prob.txt","w") as f:
#write to the file below
f.close()
#open file again as a txt file
f = open(FILELOCATION + utcnow.strftime("%Y-%m-%d") + "-" +site+"-prob.txt","rb")
ftp.storlines("STOR " + utcnow.strftime("%Y-%m-%d-") + site +"-prob.csv",f)
f.close()
reading the file as a binary file and then storing it with the storlines method removed the extra lines I was seeing within the file after I uploaded it to an ftp server.