The Bourne Supremacy background: Bourne assassinated Russian politician Vladimir Neski at Berlin long time ago but he couldn't remember full detail and recently been framed for killing 2 CIA people at Berlin.
When Nicky is sent by Pamela Landy to meet Bourne and Bourne is trying to understand why CIA is still after him, they have this conversation:
Bourne: When was I here in Berlin?
Nicky: What are you talking about?
Bourne: For Treadstone. You know my file. I did a job here.
Nicky: When? No, you never worked in Berlin before.
Bourne: My first job. In Berlin. I did a job here. You know my file.
Nicky: No. You've never worked Berlin before.
Bourne: My first job!
Nicky: No, your first assignment was Geneva.
Bourne: You fucking people!
Nicky: I swear! I swear!
Bourne: I know I was here, Nicky!
Nicky: It's not in your file! It's not in your file!
Bourne: I know I was here!
Nicky: No, I swear. Oh, please!
I don't see a reason for Nicky to lie with Bourne and it seems she is telling the truth (to her knowledge). Considering that Bourne and Nicky were close, it's also unlikely Nicky doesn't know Bourne's full experience. So, why is Bourne's mission at Berlin not known to Nicky?