What is the ruling on working for an Indian contracting company that calculates electricity costs for hospital and housing projects, knowing that the contract includes a delay penalty that the company has never claimed, and is this work considered aiding in sin?

So long as your work in the company involves permissible matters, such as calculating the cost of electricity, there is no sin upon you in that. The fact that your colleagues attach to the report a contract stipulating an usurious late fee does not affect this, as you have no connection to it and are not assisting in usury.