wood floor stains

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I just got my floors refinished. When my floors were getting done, I was not present, (wife was). As they were sanding my floors, they called me to tell me about some stains that weren't coming out. Now, from their description, I though most of the stains, (think they are pet stains) were in a area within the living room which I knew I can cover up with furniture anyway, (plus they wanted alot of money to repait it) but when I got to the house there were a couple of stains that I knew it was going to be hard to cover up. Is there anything I can do to make the stains look better, or do I have to call someone in to repair them? The floor is a light wood color