At first I had an account in stack overflow of reputation 221. The I joined Mathematica and got the reputation of 101 in Mathematica. When I came back to stack overflow I found that my stack overflow account had also received +100 association bonus. I then decided to join Physics and received 101 in Physics but this time my stack overflow account was not given +100 . Why did this happen??
you associate accounts of two or more Stack Exchange network sites, and at least one of those accounts already has 200 or more reputation: +100 on each site (awarded a maximum of one time per site)
You only get the bonus on Stack Overflow once, not for each site you join.