We can all sit here and pick the little things apart or comment on things that they had nothing to do with, but in the end only a few things matter.
1. Is the customer happy?
2. Did they get paid the contract amount?
3. When they walk away is there any additional liability.
Leaving the stairs is an issue of safety and building code. Even if they physically did not touch the stairs, a condition exists that Jim's company is directly responsible for. They constructed the patio and set the grade elevation. In doing so they constructed a landing that is part of the stair system. The chosen elevation likely had something to do with surrounding area and deck footings, etc. In doing so they caused the lowest stair rise to be well out of code, even though it appears that the other 2 already constructed risers are off as well. The solution is easy and would have cost less than $100. There is a concern and even if no one cares right now, when grandma trips it will come up and someone will be to blame.
These guys generally appear to do nice work. It is important though for everyone to look at the big picture when they do a job.