Ben Williamson put high-flying Vale ahead and while Dani Lopez headed the hosts level, Ryan Burge restored the visitors' advantage soon after the break before a Jennison Myrie-Williams penalty settled matters in the League Two clash at the Recreation Ground.
"I think we can come away with a lot of positive things," said the Shots boss. "In the first half I thought we were fantastic.
"We came up against a very clinical side in Port Vale, who are a danger, but we matched them in the first half. We're happy with the team, they have strong character but I think there were some key moments in the game which went against us.
"Danny (Hylton) has said the goalkeeper (Chris Neal) has pushed him in the area and you can't raise your hands. But the referee hasn't seen it and we have to get on with it. It's those kinds of decisions which are going against us at the moment.
"Another key moment is the second goal, which we were very disappointed to concede. We should have defended it better. I didn't think the penalty was a penalty either."