The science part of Bruce's mind wanted to analyze everything Tony said and ask questions. He wanted to know why they broke up (was it the fault of the Avengers?) and when that happened. Could Tony still be affected by it? There was just too much information he didn't know, so he wasn't sure if he could help.
Being an assistant, however, was not how he pictured helping. "I don't think the Other Guy would look good in business casual. And he doesn't know how to file, so I doubt that would be a good idea. Sorry."