Hi @connor_lough, i never had an interaction with mssql extractor, but was having a similar issue with mysql tap. Can you check what you get when you list the objects selected in the tap?
docker run -v $(pwd):/project -w /project meltano/meltano select tap-mysql --list
Hey Connor, yeah i've been there also. In some extend it makes sense as we can have the same table name in different schemas. I have this situation in our mysql instance. Glad you sorted it 🙂.