Hi WillbyMC,
welcome to the Apple (user-to-user) Community!
Re: "I upgraded my iCloud storage several months ago.
I am getting charged both the $.99 and the upgraded $2.99. Don’t know where to get this corrected".
You may want to report the issue you have:
Try signing in to reportaproblem.apple.com.
While there : you can also request a refund if you wish ...
if approved, the refund is made to the same payment method that was charged:
Request a refund for apps or content that you bought from Apple - Apple Support
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Re: "The $.99 does not show up in my purchases but I am getting billed every month for it.
I also don’t get the additional storage for the $.99. I just want it removed."
If you need more help:
You may want to reach out to the Billing and Subscriptions Support team:
There's a "Get Support -start now" link *online chat / phone / email etc.) on their website (link below):
Subscriptions and Billing - Official Apple Support
All the best :-)