appearenty the fasta file I was using had extra lines in it, although I thought I was taking care of that, but the bcftools team pointed it out and it did fix the issue that also said I could do this: cat ref.fasta | grep -v ^$ | bcftools consensus vcf.file and that would eliminate any potental lines in the future.

here is the link to the issue on github for anyone in the future https://github.com/samtools/bcftools/issues/752#issuecomment-372339708

So far, I haven't gotten an answer from the bcftools team on github but I did get two workarounds to work, the first one was to just call each segment as a region and append the cns file, which works however it is not quick. The second solution was to use vcftools with the vcf-consensus command like this cat ref.fa | vcf-consensus vcf.filtered.gz > cns.fa which I compared to the previous slow way and got the same answer so its a viable solution just need to remember the command and update some scripts. If I get an answer from the bcftools team I will post it here as well just to make a more complete answer, however the vcftools solution is completely viable.