Can I use joint compound over primer?
Yes you can overcoat the primer with more joint compound.
If you have some left just use that, but if you need to purchase more consider topping mud.
Topping mud is made for feathering places like you have and it sands just a bit easier.
In either case standard joint compound or topping mud will work on a primed surface.
Remember to prime the freshly mudded areas or it will absorb the paint and look different.