This knocking is actually banging from incorrectly or weak crossbreaks on the ductwork.
When the fan comes on, the supply duct becomes pressurized and the return duct becomes negative.
When duct is made over a certain size, it has the familiar X formed into it to prevent the noise you are hearing. If it a bad crossbreak or is weak or doesn’t have one, it’ll do that. It also may be due to undersized ducts which I have seen mostly. The contractor probably put in the smallest duct he could get away with to save money.

If you can isolate where it is coming from you can screw some type of metal bracing across it to make it stop.
Have the contractor come out and fix it.

It is probably something not covered under any warranty but it is usually easy to remedy.

Rubbing of parts or bearings