If you have a contract that specifies solid pine - yes I would dispute
the bill with the company concerened.

Decide what you most want from them - is it a bill discount? Is it
remedial work such as putting pine facings on the risers (I'm assuming
it's the risers that are mdf). Is it other work to compensate for the
difference between what you specified and what you got? Most companies
would be more willing to provide remedial work than a discount.

A possible reason is the rising price of pine - 25% in the last 5
months at my local timber merchant. As far as shortcomings of mdf - it
would be wrecked on serious water exposure (e.g. a flood) - whilst
pine would survive, and it won't take an attractive bare wood finish
as pine would, nor can scrapes and gouges over the years be sanded out
in the same way. But under carpet and in normal use, there's no real
difference.