For example, "liu" should be pronounced "liou" and "shui" should be pronounced "shuei", but the "o" and "e" are omitted in Pinyin for brevity. Similarly, the "u" in lu and mu is different from the "u" in "ju" and "qu"; the latter is actually "jü" and "qü" as in "nü" and "lü", again the diareses are omitted purely for the convenience of the writer. The "a" in "yan" and "ya"/"yang" is completely different, etc.
I like Pinyin as a reasonably concise input method, but it's not great for romanizing names.