The FCTM has a reference to the problem you encountered, it is under supplementary information, adverse weather, turbulence.
It states that during take off in high turbulence the flight crew must wait for the target speed +20 kt (limited to Vfe -5 kt) before retracting slats/flaps.
It is quite normal that S speed on take off will be almost equal to Vls once the slats are retracted, hence in turbulence you are likely to dip below Vls, that is why they recommend to keep that extra speed buffer.
Of course you will get close to your Vfe when on a heavy take off.
We only fly the A320, so S speed for us is usually much less than what you saw on that take off, but we do the same thing on the A330/A340 on heavy take off weights in turbulence.
Safe flying!