I don't know why you had that vibe, but if the guy disappeared I think it's good you spotted it early on.
Maybe you were uncomfortable due to his inexperience with poly. Not meeting someone who is familiar with poly is less threatening and scary, because you can trust they already know the situation.
With this guy, there was the chance he might assume things, turn out to be a cowboy, turn out not to understand poly at all and create drama, turn out to have made assumptions...
If he ever re-contacts her, I would suggest you keep trying to meet him, although for his own comfort, I would suggest a date in a neutral place with just him and her (with you knowing where she is) when she can answer his questions first without you being around, at which point you would join them and he could ask you additional questions, or he'd first have an opportunity to leave if he feels it's not for him.
Either way, I think you did the right thing in the end, and in the future you should try and communicate your feelings as early as possible, in a calm manner so you can discuss it.