Always ask what is it that you're not seeing.

分裂句的特殊疑问句，用作名词性从句（间接问句）时，仍然符合语法规定的使用陈述语序。所以，原句语序有误，应改为：

Always ask what it is that you're not seeing.

又如：

After all I know what it is that she loves the best. 

毕竟我知道什么才是她的最爱。

Do you know what it is that makes you so successful, film after film? 

你知道是什么让你如此成功，电影一部接一部吗？

But do we really know what it is that we're asking? 

但我们真的知道我们在问什么吗？

直接引语中，强调句的特殊问句才用倒装语序：

You may ask, "what is it that you want to do?" 

你可能会问：“你想做的是什么？