I have tried my best trying to figure out what is wrong but I could not get the solution. The description is in the pdf. Thank you for your help. I would be happy to learn from it.

 

I dont see the need for the timer based on the problem specs.
It would seem to me you want the conveyor to run any time the Proximity switch is not made or (it is made and the level switch is made) (saying the box is full) . There may be a timing issue there between the time the proximity switch doesnt see the box in place anymore and the level switch still seeing the full box. You might need a small off delay timer. Good luck and have fun thinking it through

 

I also noticed in the control logic, the WALNUT BIT SW is B3:07 and in the I/O you have it controlled by B3:05.
Looks like an error to me.