Velocity chart is basing what's included in Planned Effort based on the day the Sprint started and the Stories that were in the Sprint at that time. It does not pay attention to stories that came in later. This can be adjusted somewhat on the Velocity chart configure widget to tell it how many days before Start of Sprint is the work considered final. Scroll down on the chart widget to the below and you can adjust Days past start date.
Display planned work for iterations
Days past start date of iteration when planned work is final