Under the NEO-LAYOUT in combination with IME, the Japanese moras "DA, DI/JI, DU/ZU, DE, DO" (だ、ぢ、づ、で、ど) are not recognized. Instead, it looks like this: "」お" (for "do", the o is recognized but the d is not)
Also, the Hepburn-Romanization of じ、ざ、ず、ぞ (zi/ji, ...) can only be typed with "z" whereas under the QWERTY-Layout, a "j" is also recognized.
Finally, in combination with a German Interface, the ü becomes a k and vice versa which does not happen with the QWERTY-Layout. So when typing a mora of the k-row (ka, ki,... ), the "ü" or the "y" (Qwerty) must be used which is quite annoying.