Here are two places Muslims say the Bible refers to Mohammed by name and why.
The first is John 14:16, 26
And I will pray the Father, and he shall give you another Comforter, that he may abide with you for ever
Here is the reasoning used by Muslims based on the translation from Greek
The word “comforter” is translated from the word “Paraclete” (“Ho Parakletos” in Greek). Muslims say the Greek Periqlytos that means Ahmad or Mohammed. These are Greek words. Muslims claim that ‘paraclete’ (which is in the Bible) should be a different word ‘Pericletos.’
Parakletos in Greek is interpreted as “an advocate”, one who pleads the cause of another, one who councils or advises another from deep concern for the other’s welfare (Beacon Bible Commentary volume VII, p.168).
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Muslims say the English translation that refers to this comforter as The Holy Ghost or Holy Spirit is incorrect. The correct interpretation is a holy spirit or, in other words, a man with a holy spirit. (SP)
Additional verses about the comforter make it clear this is not referring to a man.
The Comforter cannot be seen by the world “The world cannot accept him because it neither sees him nor knows him” John 14:17
The Comforter “abides with you and will be in you.” John 14:17 Mohammed does not abide in people.
The Comforter is sent by the Father in Jesus’ name, “whom the Father will send in my name”. (John 14:26) Mohammed never claimed to be sent in Jesus name.
The Comforter ” will teach you all things and bring to your remembrance all that I have said to you.” referring to the disciples
(John 14:26). Muhammad did not help the disciples remember what Jesus taught them.
The Comforter will “be with you forever” (John 14:16).
As you can see, the Comforter cannot be Muhammad.
Again Muslims say Solomon refers to Muhammed. The word used is the Hebrew ‘Machmaddim’. Muslims claim that this word is a reference to Muhammad for two reasons, The word Machmad (singular of Machmaddim) sounds a bit like the name Mohammed and it means ‘one who is worthy of praise’ so Muslims say this is Mohammed.The context of the passage identifies the person described as Machmad as someone in the time of Solomon (Song 3:11) who is loved by a Shulamite (Song 6:13). He is red-haired (Song 5:10). None of these descriptions fits Muhammad.
Muslims also claim prophecies are referring to Christ such as this one in Deuteronomy 18:15 of the King James Bible are referring to Mohammed.
The LORD, thy God, will raise up unto thee a Prophet from the midst of thee, of thy brethren, like unto me; unto him ye shall hearken;
Muslims claim this is referring to Mohammed as Mohammed was raised up as a prophet and spoke the words given by God. However, Mohammed was not from among the Israelites and, therefore, cannot be the prophet spoken of here or in other verses.
From Matthew Henry’s commentary we read this verse is..”intended as a promise of Christ, and it is the clearest promise of him that is in all the law of Moses. It is expressly applied to our Lord Jesus as the Messiah promised (Acts 3:22; 7:37), and the people had an eye to this promise when they said concerning him, This is of a truth that prophet that should come into the world (Jn. 6:14); and it was his Spirit that spoke in all the other prophets, 1 Pt. 1:11.”
If you search the Internet, you will find many Muslims suggesting why the Bible is referring to Mohammed and even more Christian sites refuting this.
Throughout Bible history no scholar ever suggested these prophecies refer to a son of Ishmael.