Without pictures and more information it's difficult to say what needs to be done. Are you growing these pots indoors or outdoors since you repotted them? If they are indoors are they under lights? If under lights, how far from the lights and what kind of lights are you using? Do you have a fan blowing gently above the plants in the room? How tall are the plants now?
When weeding, the best way to make sure you are removing a weed and not a valuable plant is to pull on it. If it comes out of the ground easily, it is a valuable plant.