It's a cost+ contractor. I believe that's considered kablunes.
I see that the m"a differentiates between them doing it for their own benefit or for the customers benefit, this can be hard to determine, at the end of the day whatever a contractor does is for the customers benefit.
Regarding my feeling of them not listening, it was that I saw on Chol hamoed some emails with suppliers, I was out of town, but then on hoshana Raba it was confirmed to me by someone who passed by the site that he saw them working. I immediately contacted them and they explained their mistake and assured me that no work will be done second days.
As far as I know I had no suspicion or reason to believe that they did not adhere to my instructions and worked on Rosh Hashanah or Yom kippur.
In the worst case scenario, does some work done באיסור render the entire house אסור? (It's a extension/rénovation job)
Does it make any difference that it was on יו"ט שני / חול המועד?
If בכדי שיעשו is applicable, does that apply specifically to the parts of the work done or do they need to cease working on the entire project?