The subway in Boston doesn't require to tap the card to get out of the station. Thus, there shouldn't be a record of where Natasha got off.
When Maura declares she has found traces of marshmallow root, Frost checks the bar menu and says that they don't serve anything with marshmallows in it. Marshmallow root is not used in modern industrial production of confectionery marshmallows, its use being reduced from the late nineteenth century. Its replacement in modern production includes corn starch, corn syrup, gelatine and egg white, depending on manufacturer.
When the first victim (during the cold open) is stabbed in the chest, the shot with the knife being pulled out shows no blood.