Honestly, I do think you are probably jumping the gun. I don't blame you, he's your little boy and you'd do anything to protect him from harm - Lord knows there are plenty of people that are no good! You might be right about the teacher - 25 years of teaching, she decides to finish off her years before totally retiring by teaching at a small preschool, stuck in her ways, etc. etc.
I think however, you should give it some time. Definitely call her on it and talk with her. Playing devil's advocate here, she might've said "you're acting like a bad boy, let's not (fill in the blanks)" or "do you want me to tell mommy that you've been a bad boy? O.k. then, why don't you (fill in the blanks)" which aren't necessarily as bad as what you are probably thinking (ie "Johnny, you're such a bad boy!")
Don't forget, kids have selective hearing! She might've used "bad boy" in a sentence but not used it in that context with him. Since you mentioned it wasn't something that you use at home, it might've stuck out to him and that's what he remembers. He's not lying to you, he just might not have phonographic memory!
As far as talking with her about it, since she's the boss at this school, she might be defensive, but then again, she might be very open minded! You won't know until you talk with her. Definitley try to talk it over in your mind before going in so you don't sound like you're on the attack. The last thing you need is for the teacher to think you're some overprotective mama who wants special treatment for her kid. I'd actually recommend talking with her in front of your son. This way, you can show her you're on her side by getting to the bottom of this as well as sneaking in what you'd like to hear her say to him next time, and to top it off, show your son that you expect him to behave for the teacher.
Tell her that your son mentioned that she had called him a "bad boy" a couple of times and that it really bothered him. Tell her that you told him you were going to talk about it with her so that you could find out why she thought he was bad. When she tells you the story, you can support her by agreeing that what he "did" was bad and that he shouldn't have been acting that way. Finish it off by telling your son, in front of the teacher, that "she doesn't think that you're a bad person/bad little boy, she was trying to say that it was a bad thing to do (fill in the blanks)". Maybe finish it off by saying "you're a good boy, right? Do you think good boys should do (fill in the blanks)? No, of course not. Why don't you apologize to your teacher for behaving that way and tell her you'll try to make better choices next time"
After you have that dialogue, if you still get the sense that she called him a "bad boy" and he didn't misinterpret, you can pull her aside, if you feel comfortable, and tell her that you and your husband try to talk about their actions being bad and not that the child is "bad". You can always lie and say that your older son had some major issues with that and you want to avoid the mistakes you made with your first son. Total lie, but at least it won't make her think you're just being defensive.
Make sure to update and let us know what happened!