Pumping ruining breastfeeding?

Ash • Married 8.2.2014. 1st Boy 11.24.16. 2nd Boy 8.27.18

I've had to pump and give a bottle a lot lately for various reasons. I'm noticing that my son isn't emptying my breasts. He doesn't seem to eat enough while breastfeeding and then wants more within a half hour. It's also still taking him 45 minutes to eat but he's not even filling up. Is this because I've had to give him bottles? I can I fix this?

My son is almost 6 weeks old. I've dealt with cluster feeding before, this is different. Like he's just not getting enough or something.