两种表达都正确。众作周知，到达一个国家、城市等较大的地方时，多用arrive in，所以通常要说arrive in Beijing；到达小地点多用arrive at，但如果把北京作为一个点或途中的一个站，则也可以说arrive at Beijing。如：

The train from Beijing to Guangzhou will arrive at Wuhan at 7:30am.由北京开往广州的列车将于上午7:30到达武汉。

(1)arrive in +大地方(国家/城市)强调某人/某物进入/达到某个地方之内

When did you arrive in Beijing?

It was the cold season when I arrived inGermany

(2)arrive at +小地方（车站，机场；城镇）；强调某人/某物到达某地之点。arrive at 表示做出某个决定

if the jury cannot arrive at a unanimous decision.

These figures are arrived at on the basis of dentists' receipts for 1991-1992.

The Princess Royal arrived at Gatwick this morning fromJamaica.

We arrived at the Shanghai Railway Station at 11:00 pm last night.

When we arrived at Wuhan Airport, it's midnight.

我的问题是 

1. has probably arrived 和 probably has arrived 都正确吗？    

 2. arrive at Beijing 用在这里对吗？

继续回答如下

(1)副词probably在句中所放位置有以下2种情况

 A.一般放在系动词之后，行为动词之前

Van Gogh is probably the best-known painter in the world. 

凡·高可能是世界上最知名的画家。

He probably thinks you're both crazy! 

他可能认为你们两个人都疯了！

 B.一般放在助动词之后，行为动词之前；或者动词某种形式之前

Tom will probably visit you tomorrow.

汤姆明天很可能要看望你。

He has probably seen the film.

他很能看过这部电影。

arrive in 表达达到某个地方之内

arrive at 除了表达达到小地点，还表达到达某个之地.

arrive at Beijing 表达到达北京之地