Indents are made in two ways. On a free blown sphere, the glass blower plunges a carved stick into the ornament while still hot. The glass conforms to the shape of the carving and the molded shape of the indented portion appears. It is also possible to find indents that have been mold blown. In this case the design is carved into the mold. Here are examples of each from my recent auctions:
Free Blown Indent
Mold Blown Indent