One problem related to manual transmission has been reported for the 2003 Honda Civic Hybrid. The most recently reported issues are listed below.
My car has a manual transmission. The auto-stop feature cuts in sometimes when I shift into neutral preparatory to downshifting to accelerate. If this happens when I am trying to make a left turn through a break in oncoming traffic or pull into a gap in traffic on the expressway, it can be quite frightening. Fortunately, I haven't been hit yet, but my wife is reluctant to ride in my car. There was a recall several years ago which the Honda serviceman told me would fix the problem, but it didn't.