I am trying to use remove.rare to remove any OTUs that have less then 10 sequences. I am using remove.rare(shared=, count=, list=, nseqs=10). However when I do get.oturep I am still getting OTUs that have a less then 10 sequences.

Did you include the count file with the get.oturep command? Remember when you are clustering with the list and count file, the list file only contains the unique names because the count file only contains the unique names. The remove.rare command will use the count file information when determining whether an OTU is rare.