Regarding HSL's journey planner this routing error seems to appear in the current OTP1-version. We at HSL are planning to update to OTP2 during March. The new version will more efficiently handle these kind of routing islands. So that might be one solution to the problem as well. However adding the connection to the inner yard is highly reccomended if there is one. btw. OTP = OpenTripPlanner, which is the routing engine we use within our journey planner.