Hello JeremyVero,
Thank you for using Apple Support Communities!
I understand from your post that numbers that have called you but are not saved as a contact are automatically defaulting to your secondary number. Is your secondary number the default number? If so then that may be normal according to the following article:
Using Dual SIM with an eSIM - Apple Support
"If you haven't called that contact, your iPhone uses your default number."
In order to make sure that the number being used is the number they used to call you, you would need to save them as a contact and assign which number you want to use to call that person.
In regards to the voicemails showing that they are from the secondary number even though that is not the number they called from, check to see if you have call forwarding enabled as that will forward the call to the primary number which may make it look like the call came from that number.
Best Regards.