Flaps retraction
The flap retraction schedule is one step up every time. This step is based on the way the flap lever is designed by Airbus.
Next time you sit in the cockpit on the ground, take flap levers to FULL and then try retracting them. The lever will first stop at flaps 3 position and then you will have to again lift up the lever and take it forward. Now it will stop at the flaps 1 position. It is designed not to stop at Flaps 2. Now you will have to lift up the lever again and retract flaps to 0.
Now when you sit in a flying aircraft, look at the F speed for Flaps 2 and Flaps 3. The F speed is the same for both positions. So when you are doing Flap retraction from Flaps 3 on schedule, there is no reason to stop at Flaps 2 and then get to Flaps 1.
The one step up which Airbus refers to is the step of the Flap lever position the way it is designed and not Flaps 3 to 2 to 1.
So what your instructor is telling you is correct. Retract Flaps from 3 to 1 every time.
Also, refer to the normal operating procedures for Takeoff in the QRH.
AT F SPEED
FLAPS 1 ......... ORDER
So, whether you do a Flaps 3 or Flaps 2 Takeoff, the retraction schedule is Flaps 1. This is also applicable to GA phase. Retract one step means, from Flaps full to flaps 3 and from Flaps 3 to flaps 1.