After she took the first shot, it probably took her at least a second to assess the situation and make the realization that she hit someone and they had fallen off of the train.
Then she would have had to take more time to see that she had hit Bond, not Patrice. It would have been difficult to see this easily through the scope of the gun, and the train was too far away to see clearly without the aid of the scope (as they were wearing similar clothes, were similar build, and would have been almost indistinguishable from afar). That's another couple of seconds.
Then she is probably incredibly shocked at the fact that she has just shot, and most likely killed, not only a fellow agent, but a high ranking fellow agent. The implications of this (concern for Bond, getting fired, failing the mission etc.) would take another second or two to rush through her mind before she can at least recover enough to make a decision.
It would only be at this point that she might consider taking another shot to take down her intended target. By this point the train is no longer moving towards her (allowing her an easy shot), but moving very quickly perpendicular to her. This would make Patrice an incredibly difficult target to hit, even if she had attempted to shoot him again.
She may then need to take more seconds to assess the risk of spraying bullets wildly to try to hit her very fast moving target. Remember he was stood on top of a packed commuter train, she could have caused a lot of collateral damage if she was inaccurate. She didn't have nearly enough time to realign herself to pull off an accurate shot even if he hadn't have been a moving target.
By this time the train is gone. She has missed any opportunity that she had to correct her mistake.
This is all predicated on the fact that she is thinking clearly, however she is in an incredibly stressful situation. All this from someone who is, as she says herself at the end of the movie, not cut out for field work. She was simply too inexperienced and unprepared for that situation, one in which a top agent would likely also have struggled with.