There is a known issue with the Funcotator germline v1.6 data resources. For some variants, the protein predictions are wrong. We are detailing our observations at the github ticket here. If you have seen examples of this issue, please comment on that ticket so that our developer team has more examples for troubleshooting.
We have already released the v1.7 data resources and we recommend that users upgrade and do not use v1.6. You can find the details on how to download new data sources at our Funcotator Information and Tutorial article.