Hi six, welcome to the forum.
When you hover your mouse over a wild plant there is an option for your sim to dispose of the wild plant. (i.e. a lemon tree growing anywhere that is NOT your home lot). If you dispose of a wild plant and then hang around that neighbourhood for some hours then the wild plant will regrow. If you go to
Carl's gardening guide page and scroll down you'll see a table that tells you how long each plant takes to grow so you'll know how long you need to wait in the neighbourhood for that particular world plant to grow back.
The only other thing I can think of is maybe you have some CC that is causing the issue although you've said you have no mods. Obviously there are no pomegranate trees in the wild so if disposing a wild lemon tree makes it grow back and grow fruit then you might just have to delete your home trees and get the plants you are missing by grafting or fishing up a pomegranate. etc.
*edited opps I read your post wrong and thought the wild plants were not growing fruit... never mind, one of those days!