Since your question does not focus on any specific claim, I will address only the general genre of claims that are made on this topic.
I hear two genres of claims being made about Mohamed and Islam in relation to the Scriptures.
- Texts containing relevant information and teachings not present in the accepted canon of Scripture have been excluded from Christian study. This claim usually centers around the (re)-discovery of various ancient texts documenting the beliefs of various historical groups that held teachings heretical to Christianity.
One such example can be seen in this news article. In reference the recent find a well preserved copy of the Gospel of Barnabas being discovered last year in Turkey:
A 1,500-year-old Bible in which Jesus is believed to have foretold the coming of the Prophet Mohammed to Earth has attracted attention from the Vatican this week.
It's important to note that this article isn't well researched. The find is not a 1500 year old Bible, it is a possibly 1500 year old copy of a book purporting to be the Gospel of Barnabas, which is NOT EVEN CONSIDERED PART OF THE BIBLE. While Barnabas was one of Jesus' disciples and the claim is often forwarded by skeptics that the testimony of someone in that position should not be ignored, the currently suggested date for the manuscript in question is hundreds of years after the texts we have from other apostles and it has not been established that this book even represents the teachings of Barnabas. Seeing as how the witness is also contrary, it makes little sense to hold these writings in esteem not granted to the earlier accepted manuscripts.
The article goes on to point out two claims:
“In one version of the gospel, he is said to have told a priest: ‘How shall the Messiah be called? Mohammed is his blessed name.’
“And in another, Jesus denied being the Messiah, claiming that he or she would be Ishmaelite, the term used for an Arab,” the newspaper added.
As noted above, however oft-repeated these claims may be among those skeptical of or opposed to Christianity, they are not based on documents that have any credible bearing on Jesus, his teachings, or the foundations of Christian faith. It is well accepted in Christian circles that even during the early church there were all sorts of heretical groups around teaching all sorts of divergent things about Jesus. These teachings were systematically rejected as being contrary to the plain and verified teachings of Jesus as witnessed by those closest to him. The re-discovery of ancient documents from these divergent groups poses no threat to Christianity, nor should their doctrines be taken as having any bearing on Christian doctrine.
- Words present in the original language text that point to the coming of Mohamed or of Islam have been misinterpreted either deliberately or though lack of understanding. There are several variations on this claim using different words from various passages.
The most common one centers around the Greek world
Parakletos, particularly in the John texts. The argument takes about a dozen different forms, but the gist of it is that the Greek text, being a translation of what Jesus would have actually said in Aramaic is confusing and misleading. The claim is that rather than being a reference to the Holy Spirit (this third person of the Trinity, promised by Jesus to come after he left and act as an advocate leading us into truth) this should actually be interpreted as a reference to a later prophet. The claim often includes an accusation that biased later generations of Christians only introduced the idea of the Trinity in later copies and translations.
These claims simply do not hold water and are rejected by all Christian teaching. One of the principles we use for interpreting Scripture is using other more clear passages on an issue to shed light on any that we are not sure how to understand. We also use the interpretations of people present (i.e. the disciples for Jesus teachings, etc.) to help guide our own. In this case the verses in John that are in question are clearly and concretely demonstrated to be talking about the same Holy Spirit that was given at Pentecost and dwells with believers. Furthermore, any attempt to render these passages in a different light ends up making a massive mess of the rest of Scripture turning it to testify against itself (a pretty sure sign you've read it wrong).
Another example sometimes cited is in Isaiah where several tributes to a coming elect servant are given. While Christianity universally understands these as describing the coming Christ himself, they don't bear a name. One of them intros "Behold my servant, whom I uphold, my chosen, in whom my soul delights." An argument is sometimes made that "my chosen" or in context, "God's chosen" translated into Arabic is "Mustafa" (true enough), then claiming that nobody had that name until the founder of Islam came along. Never minding for a minute how many people have the name even to this day, a name alone isn't enough to tie somebody to a prophecy especially when the other parts of the prophecy don't match. Isaiah includes many specific descriptions that even Muslims don't try to interpret as being fulfilled in anyone but Christ. Some of those prophecies being re-directed on a linguistic twist isn't something Christians acknowledge as a link.
While the above are simply some of the possible examples of this, the universal conclusion of Christian scholarship (and hence, doctrine) is that such techniques represent a poor hermeneutic, not taking into account the whole of Scripture, forcing items out of context and rendering the text to say something it was never meant to say.
Christianity universally and categorically denies that any texts outside of the canon provide an authoritative witness to Jesus' teachings and that the words brought into question as possible references to Mohamed or Islam have anything to do with the subject. On the contrary, any such teachings are expressly contrary to the vast weight of scholarship on the issue. It is not a point of common understanding between faiths, and anything built off of such a "bridge" invariably ends up being contrary to other Christian doctrine.