What's with Marissa's bleeding gums in Hanna?

My take on the situation is she has an Obsessive Compulsive Disorder (OCD). As explained in Wikipedia, this disorder shows in a lot of different ways. One such:

The acts of those who have OCD may appear paranoid and potentially psychotic.

Agent Marisa displays both of these traits in the movie. Also, she is very fastidious in everything she does (overly clean and particular). I don't think she is full blown OCD (if you read the Wiki article, you'll see what I mean), but she does show many of the symptoms. Considering the flossing behavior is over the top to you and me and she does this more than once, it might be considered this type of behavior. I am sure there are other things in the film which point to this as well, but not popping into my head at the moment.

The reason these scenes are important is because it develops the character to show you she has problems with things she has done in the past, whether or not she realizes it.

Yes, it does show she has problems with her past and feels guilty.

Plus, you might add it's also a fairy tale: she's the Bad Wolf, compulsively cleaning her teeth of her preys' blood, which only makes them bloodier (see the final scene when they literally run "into the wolf's jaws", and Hanna turns the tables on her and hunts her down).

According to this article

Wright created the teeth brushing scene as a joke about the U.S. obsession with teeth. As a Brit with bad teeth, he feels “slightly resentful” of Americans’ perfect choppers.