Assalaamu alaykom.
{In it are clear signs [such as] the standing place of Abraham. And whoever enters it shall be safe.} I am unable to understand that Allaah said (what means): {And whoever enters it shall be safe.} while I always hear that many people (pilgrims) die during the Hajj. That sounds strange to me; as if we are doing something wrong. Can you please help me understand this verse? May Allaah reward you.

All perfect praise be to Allah, The Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad, sallallahu ‘alayhi wa sallam, is His slave and Messenger. 

The verse: {And whoever enters it shall be safe.} [Quran 3:97] means, 'Whoever enters it, grant him protection.' The verse is intended as a command to grant protection to whomever enters the Sacred House, but it is in the form of a statement (a report). It means that it is obligatory to give protection to whomever enters it and not to harm them in any way. This style is frequent in the Quran. The author of At-Tahreer wa At-Tanweer said, “This is a command phrased as a statement; it means that whoever enters it should be granted protection. It is similar to the verse that reads: {Divorced women remain in waiting for three periods.} [Quran 2:228] It means that the divorced women must observe their ‘Iddah (post-divorce waiting period)...”

As for the past or recent accidents and events that took place in the Sacred House and caused the death of some people, this does not contradict the verse in the slightest. In fact, this very misconception was raised by the enemies of Islam long ago. Al-Qurtubi commented on the verse, saying:

“An atheist once said to a scholar, 'Does not the Quran say, 'Whoever enters it shall be secure?' We have entered it and done such-and-such harm; how can the Quran be true?' The scholar replied, 'Is not Arabic your mother tongue? When someone says, 'Whoever enters my house is safe,' and someone enters his house and then another attempts to harm him, would the owner of the house not say, 'Do not harm him for I have granted him protection'?' The atheist replied in the affirmative. The scholar remarked, 'This applies to the verse in reference as well. It means that whoever enters it (the Sacred Mosque) is granted protection and security.'”

Allah knows best.