I think you might be out of luck with the rabies thing. Around here, if you let their rabies shot expire before getting them vaccinated again, even if you only wait a day, then the vets won't give you the 3 year shot. To get the 3 year vaccine here, you'd have to get your dog vaccinated before or exactly on the expiration date of their last vaccination. So yeah, I'd guess that because he was overdo that's why they only gave him the 1 year. That's how they'd do it around here as well.
Next year, take him back for his shots a few days before the vaccination expiration date on his rabies certificate and then you should be able to get the 3 year.
The other stuff just sounds like stupid mistakes. I had that happen to me once before, Kitsune was listed as "not altered" even though he's neutered, and they tried to charge me more for his license. I had to go home, get his neuter certificate, then go back again.
If you already got the license then it's probably not a big deal but if it where me I'd probably call or go in and try to get everything corrected just in case.
To view links or images in signatures your post count must be 10 or greater. You currently have 0 posts.