How do Cobol's agents know Cobb was in the Mombasa motel?

As with so many plot points in Inception this is probably designed to cloud our understanding about whether Cobb is in the real world or in a dream. You could easily say that Cobol Engineering are obviously a very powerful and ruthless company - they were willing to hire Cobb's group to steal ideas from a competitor, and are willing to kill Cobb for his failure. It seems that they would be the sort of organization that could hire investigator to track Cobb, and would be willing to pay for information about his whereabouts.

Later in the movie, Mal (well probably Mal's projection) suggests to Cobb that he doesn't really know what reality is. She points out that it is odd that he is constantly pursued across the globe by powerful organizations. The suggestion is that Cobol's agents are acting like projections - hunting Cobb down like he is the architect in someone else's dream.

So you can take your pick - they are either a powerful and well informed organization, or they are merely projections of someone else's subconscious.