I am wondering if there was some substance put in her coffee, which could then explain the overturned coffee cup, glasses on the floor, and the table shifted. Maybe Holly dropped to the floor, then the perp took her?
I am wondering when the coffee was made, before or after she took her son to the bus stop? If it was made before she left, a person could then have put meds/poison in the pot or cup of coffee. She could have heated the cup of coffee in the microwave, if it got cold, perhaps, or was the coffee maker still plugged in and on? Maybe the person broke in after she left to go to the bus stop, or they were hiding there all along, waiting for her to get back?
Obviously,with the coffee cup overturned, table moved and glasses on the floor, something happened, whether there was a person in the room at that moment, or not.
This could explain why nobody heard screams, etc. She was knocked out cold, perhaps.
IMOO.