The pens are scattered around some new NPCs will have appeared and other NPCs will have different dialogue for you.
I would recommend downloading a new version just in case as there was an issue with the pens a while ago
The green pen can be obtained in classroom A0-2 by talking the girl with black braids. the red pen can be obtained by talking the the brown haired bob girl in classroom A0-1 and the yellow pen can be obtained by talking to the girl that spawns just outside the art room.
hope this helps.