Okay so I went back and spoke with the manager, I let him know what happened and he actually seemed pretty concerned. I like that he was annoyed because it shows he cares. He was annoyed because he wasn't there when I got such shitty service so he wanted to know exactly who did what and why.
As for the punch card issue, the girl that rang me up was new so I guess she didn't really know how to look up my phone number because he found it right away and like she said, he linked my new account with our old one.
To top it off he gave me a free upgraded car wash, good for 1 use anytime. I'm really really happy with this place, this was definitely 1 of my loyalty tests, how well you handle complaints says so much about you, your business, your policies etc.