I`ll never understand how it --- that you were an hour late

首先来分析一下这个句子地成分：how that you were an hour late on such a short journey 是这个大句子的宾语从句.it是形式主语,而you were an hour late on such a short journey 才是真正的主语.实际上就是 you were an hour late on such a short journey这件事情发生了.如果你用caused的话,那么它“引发”了什么呢?因而这个宾语从句就没有宾语了.所以要用came about而不是caused.