I seem to have a phobia of germs since my brain injury I was never like this before I got injured it really bothers me has the brain injury caused it?

Possibly. brain injury can cause anxiety disorders. What you are describing is a symptom of Obsessive Compulsive Disorder, an anxiety disorder. So yes, brain injury can cause your symptoms.
Phobia After TBI. There are many published reports of persons developing anxiety problems after sustaining a traumatic brain injury. You are among the subset that have developed a specific phobia. Luckily, we know about how phobias can be overcome! Learn about phobias & how to rid yourself of them using "exposure" techniques & systematic desensitization: http://www.anxietybc.com/self-help/facing-your-fears-exposure.