Hello,
First I would like to say that chances are this is an inocent situation and there is nothing to fear.
You are the spouse, you are required by contract to be nice and say nice things.

Anything you say while it sings to the heart can be hard to take to heart. Your words are suspect in that you are the last person in the world she figures will say something that is likely to hurt her.
I have this issue myself. My wonderfuly awesome and epic spouse Sevan can tell me till ze is blue n the face how pretty I look but there is always that worry in the back of the head that says 'Sevan is my sweety most, ze see's me through rose collored glasses'.
I don't want it to go there but it does.
As to the man flirting with her ...
You know very well how much a woman vests into her apearance and her percieved value to men. For right or for wrong (trust me its wrong) we all do it. She is a woman who has soaked up all the same messages about being a woman in this culture that every other woman has. This man flirting with her was a validation of some form. A man paid attention to her.....probably the first time in her life. Think on that for a bit.
Anyways...
She does not know all the girl rules of engagement with strange men. She can get herself in a bad situation very easily as she is not aware of the red flags to look for in guys. This would be a good area for you to fill her in.
Best of luck.