During construction it is important to verify that your contractor is protecting your mechanical and plumbing system from contaminants. Not protecting these systems can be harmful to the systems and your health. There are two types of contaminants that you generally want to protect against.
First, objects that may fall into your plumbing or mechanical systems and become lodged or block up the system. This is fairly simple to protect against by capping or covering all open pipes and registers. I’ve seen contractors only cover to keep people from falling in, make sure the entire opening is covered.
Second, you want to protect your mechanical system from dust, allergens and debris. This is especially problematic in remodels where the system may be running in other portions of the building and sucking dust into the system. This is typically accomplished by installing plastic and tape over the registers and closing any dampers. Where it is not necessary to run the mechanical system during construction it is advisable to turn it off.