This sounds like a misunderstanding.
If he speaks in english as a native german it is his misunderstanding, if he speaks in german it's probably yours.
Referring to people as "Mitarbeiter" literally translated means co-worker but can also mean employee, especially if introducing to a third party who knows he is the owner or upper management.
The literal translation of employee would be "Angestellte(r)".
I doubt that's how he addresses you personally as it does convey the hierarchy and is, while technically correct, somewhat misplaced or rude.
It is however absolutely acceptable to introduce you to a third party this way, provided he is the owner or upper management.
If he is a new business owner he could express his pride this way.
In germany, addressing an employee directly is usually done formally using the last name and putting "Frau" or "Herr" in front of it.
Lately, especially in young companies your first name is used in an informal way of addressing one.