The answer is as follows:

First (1), this gives the impression that He (2) mentions this in several places, whereas that is not so: He mentions it only in the account of Hunayn. As Allah Most High says:

“And on the day of Hunayn, when your great numbers pleased you but availed you nothing, and the earth, despite its vastness, became straitened for you; then you turned back in retreat. Then Allah sent down His tranquility upon His Messenger and upon the believers, and sent down forces you did not see.” [Surah al-Tawbah: 25, 26]

Thus, He mentions sending down tranquility upon the Messenger and the believers after mentioning their turning back (3) in retreat.

He also mentions sending down tranquility upon the believers without including the Messenger alongside them, in the passage beginning with His words:

“Indeed, We have granted you a clear victory.” [Surah al-Fath: 1]

And continuing to His words:

“It is He who sent down tranquility into the hearts of the believers.” [Surah al-Fath: 4]

And the remainder of the verse; and in His words:

“Allah was certainly pleased with the believers when they pledged allegiance to you under the tree. He knew what was in their hearts, so He sent down tranquility upon them.” [Surah al-Fath: 18]

Second, it may also be said that people have differed over the referent of the pronoun in His words, Most High:

“Then Allah sent down His tranquility upon him.” [Surah al-Tawbah: 40]

Some say it refers to the Prophet, peace and blessings be upon him. Others say it refers to Abū Bakr, because he is the most recently mentioned of the two and because he needed tranquility to be sent down upon him (4). So He sent down tranquility upon him just as He sent it down upon the believers who pledged allegiance to the Prophet under the tree.