A note here, the adjective An uses for "funny" is "面白い" (omo-shiro-i), which can be interpreted in several different ways.
It's typically used as a positive adjective for things one finds interesting, amusing, intriguing, fascinating, engaging, essentially saying something is unusual in a positive but amusing or curious way.
It can also be used as a more subtle backhanded way of saying something is odd or out of place. (It's not being used like that here, mind you.)
An likely simply means "he's a fun person to be around", but using this word means in a way everyone can hear what they want to hear in what she said. All of which add up to her saying that he's "unusual but in a positive way".
Combine that with the little chuckle before saying it, if I were those guys I'd have the exact same reaction. It's hopeless.