Angry Fish

Hi everybody, I'm new here and wanted to get to know a little more about my Betta. I've had Fishy for about a year and a half now and have fallen in love with all the little things he does. He currently lives in a 3 gallon tank with a fake tall plant and a Spongebob Pineapple house. Up until about a month ago he was always happy to see me swimming up and down and side to side. Now he still swims up to me but full gills flared. I thought it was temporary but he hasn't stopped. He stops doing it to eat his food but as soon as he is finished he goes back to flaring. I haven't really changed his feeding habits or anything. The only thing I've done differently is use a net to catch him when changing the water in his tank. Before I would just pour him into the cup he came in. Could he be mad about that? Its been a little while so I figured he'd forget about that kind of thing after some time. Do bettas hold grudges? And if so how do I make it right? :-(