I am not a home builder, but my guess is...
They did not glue down the subfloor. Running a bead of liquid nails on the joists just before you lay down a sheet of plywood greatly locks things together.
The joists are simply too small, or not properly anchored at the ends.
There is no cross bracing between the joists. This will leave them more flexible.
All of these things will help to stabilize a floor. When the various members are solidly locked together, your house will be come quiet and stable.
You might go into the basement and look carefully at what happens when someone walks heavily around upstairs. What is flexing? How is it moving?
Definitely talk to an inspector or engineer to get a good explanation of what was done wrong. Find somebody you can trust. Of course, getting the builder to make it right will be difficult, and anyway do you really trust the cheapskate to do it right even then?
Were it me, I might consider adding a sister beam alongside a few of the existing joists that are flexing. You can even use liquid nails to glue it to the subfloor when you put the sister beam in place. This will stiffen them. Add cross braces, in the shape of an X between the joists. For a few hundred dollars out of pocket, you can do a great deal to reduce the problem.