Hi derek,
Very good question and something we should all be aware off.
Make sure you are not over wetting the carpet in the cleaning process,check your machinery is not faulty.
What you are describing is known as relaxation shrinkage.This occurs when the strained yarns relax after the stress placed on them in manufacture is released. "Usually" when dry the carpet will return to pre cleaned condition (rugs can sometimes take a little longer).
Warp yarns , the ones that run in the long direction, are under tension when carpets are manufactured at the mill.When they come into contact with moisture they tend to relax and waves appear on the carpet.The Weft that runs from left to right is not under as much tension
so as the warp relaxes it buckles against the weft causing the waves.
Hope this goes some way to explaining what is going on and as you have noticed every thing normally returns to normal.
Simple response to customers worried looks is to say you will call them the next day to check all is well.This assures them you know what you are talking about and are a responsible cleaner.You will keep this customer as they will trust you.