下面两句一点问题都没有：

He thought they would leave in 3 days.

He thought they would leave 3 days later.

但下面这句读起来有点怪怪的：

He thought they would leave after 3 days.

我的感觉是after通常应以过去或将来的时间为基准。举两个例子吧：

It will be difficult for you to smooth over your differences after so many years. 经过了这么多年，你想消除你们之间的分歧谈何容易。

I’ll try to get there on time tomorrow but, if I fail, wait for me, please, I’ll sure arrive after a few minutes. 明天我会设法准时到达那里，但是若是我没赶到，请等我一下，过了几分钟我一定会到。