Duplicates of the same gene in Orthogroup sequence files

Question

[niconps14]

I'm using the orthology inference program OrthoFinder, and in many of my Orthogroup sequence files, within the same orthogroup I am getting duplicate copies of the same exact gene, with identical identifiers and amino acid sequences. My original fasta files that I input to the program do not have these duplicates, nor do the trees corresponding with the orthogroups. Does anyone know what could be causing this?