So Phineas came to my town today to give me the silver seafood badge but I also think that I need the silver catalog badge since ive filled with over 50% in the last few days and I have also picked over 500 weeds for the weeding badge. Does phineas give you one badge a day and then come the next day to give you another? Or do you pester him until he gives you other badges?
He only gives you one badge per time you talk to him. If you're sure you meet the criteria for those other two badges, you'll need to talk to him two more times.
He gives one per conversation, so if you feel you've earned more, just hit him up for a new chat and ask for another badge. If you've earned another, you'll receive it. If not, it'll just be idle chatter and you'll know to keep working at whichever badge you thought you earned.