If he wanted to talk to you about your academic progress, and this was an appointment in his office, I wouldn't give it a second thought. It is common for professors to have meetings in their office, one to one.
Oh I was interpreting this as a junior in college, but I think maybe you mean high school. Where was this meeting held? Did he only talk about your education?
It would take something more than him being alone to make me uncomfortable or suspicious. But for future, you can always suggest a public place, like the cafeteria.
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A finger in every pie.