No, difficult terrain does not stack
Every foot of movement in difficult terrain costs 1 extra foot. This rule is true even if multiple things in a space count as difficult terrain.
An area is difficult terrain or it is not. But there is no area that is more difficult terrain by virtue of having stacking difficult terrain effects in it.
Regardless of the amount of effects that cause difficult terrain in one area, moment costs 1 extra foot per foot of moment.
Your specific case
In your case specifically, the floor appears to have been a special case of difficult terrain that cost even more movement to get through:
The water in the central area of the floor is 2 feet deep, and the floor is very slippery-moving across this difficult terrain costs 3 feet of speed for every 1 foot traveled.
This is a case where the specific (the adventure module) overrules the general (the PHB difficult terrain rules) and allows difficult terrain to cost 3 feet of moment per 1 foot moved. However, this does not overrule the fact that difficult terrain still does not stack. Thus, the difficulty from walking through another creature's space would not add to the movement penalty.
Though not explicitly stated in the rules, it seems to be the most logical to choose the greater effect (the slippery floor) over the lesser one (moving through occupied space). Not only is the floor effect greater in magnitude, but it is also permanent and effecting the entire area. The penalty for moving through another creature's space is local and conditional.