God doesn't, but men often do.
Is there a numerical system in scripture and if there is, who put it there?
What do you mean by "numerical system"? Sure, God uses numbers in His word to teach truth; forty days, seven churches, twelve tribes/apostles, one hundred forty four thousand sealed ones, one thousand years, etc. He put those numbers there, out in the open and clearly understandable.
So-called Bible codes are a different issue.