So I've done some more digging, and it turns out I have Dual Indexed Barcodes. There are forward and reverse barcodes for each sample. When looking at both the F and R barcodes, each sample has a unique pair, but the F or R barcodes themselves are not unique to a given sample. The image below shows the barcodes for my first 20 or so samples. As you can see, the combination of barcodes is unique, but it reuses individual barcodes. Apparently it is helpful for doing more sequences on a single run.
When I run the cutadapt command it is failing to demultiplex properly because it is looking for unique forward barcodes. Only 24 samples are making it through because that is the number of unique forward barcodes that I have.
There is a post here from @Lusanto that explains how they managed to work around this issue (Post #17 of 26). I'm going to attempt to use their workaround to see if I can get it to work.
If anyone else has found another way to get qiime2 to demultiplex Dual Indexed Barcodes, I would be most appreciative of any assistance!