There is no contradiction at all in the accounts of the arrest of Jesus. The details in each of the gospels complement rather than contradict one another. Ally can say what he wants, but unless he can show an actual contradiction (he cannot) this is mere rhetoric. In all accounts, Judas led the one arresting Jesus. In all accounts Jesus willingly submitted himself to being arrested. In all accounts, he was taken by force. In some of the accounts (Matthew, Mark) the apostles fled and abandoned Jesus. Some accounts (Matthew, Luke, John) report Peter cutting off the ear of the soldier, while others (Luke, John) report Jesus healing that ear. Where is the contradiction? It is in the mind of Shabir Ally. This is quite simply a bogus claim. As for carrying the cross, the solution is quite simple and people ought simply to stop making this obviously false claim of a contradiction. Jesus carried the cross-beam a certain distance, but due to the weight of the beam, and due to exhaustion from his beating, he could not carry on, so a man named Simon from Cyrene took it the rest of the way. Seriously, this is supposed to be a contradiction? The next contradiction is also only in the mind of Shabir Ally. Jesus told his disciples and us that he would suffer and die for our sins. He also said in John that he willingly did this. A contradiction? Again, only in the mind of Mr. Ally. Shabir says that in Acts Jesus appears to Paul as a spirit but not as a physical body. I just read the account in Acts 9. It does not say this. Did Ally make this up? Where did he get this idea? It certainly was not from the Bible. He tells us that Jesus appeared to his disciples as a spirit. When and where? This is in the mind of Shabir Ally, but not in the Bible. By now you ought to be recognizing that Shabir Ally is not a reliable source on these questions. His bias is so obvious, you ought to begin to doubt all he says.
Do we have sources outside the Bible that Jesus was crucified by the Romans? Yes we do, but even if we did not, there are hundreds of eye-witnesses, as mentioned in the Bible. Is Shabir Ally proposing that they are all liars? Did they all die for a conspiracy theory? Is this a reasonable proposition? I do not think so. But we do have outside reports of his crucifixion, specifically from Cornelius Tacitus, a Roman historian and from Josephus, a Jewish historian. Of course, neither of these were eye-witnesses, but both report that Jesus was crucified in Jerusalem under the authority of Rome. The crucifixion of Jesus is about as historical an event from the ancient world as we have. Even Muslims agree that a crucifixion happened–they just claim that they crucified the wrong person. Can any reasonable person believe this nonsense?
As for the deaths of the apostles, we do not have reliable accounts for most of them. The means and place of death of Paul, Peter and John are well-documented, whereas the information on the other apostles is not well-documented. But how is this important? Why do we need to know how Andrew or Thomas died? Why does that matter to Christianity? It does not. The fact is that at least two of them were killed for their faith–Paul and Peter–and it is likely that several others were as well, giving us strong evidence that they believed their own testimony about the death and resurrection of Jesus, but we do not happen to have strong evidence one way or another.
Mark does report the resurrection in Mark 16:1-8. What are these people trying to say? It is true, that Mark 16:9-20 are likely not to have been part of the original Mark. True, but this is just a smoke screen. Mark, like all the other gospel writers, tells us that Jesus was raised from the dead. The fact that the exact ending of Mark is not certain does nothing to this and claims that this makes the resurrection uncertain is a red herring argument. These critics are saying that Mark did not report the resurrection. Read Mark 16:1-8 for yourself. They they say that the later gospels fabricated the story. Luke was written in about AD 63 or 64. This was just a few years later. Matthew was also written in either the 50s or 60s AD. Again, just a few years later. Are Muslims proposing that these two made up the story of the resurrection, only 20-30 years after it happened, when most of those in Jerusalem at the time were still alive, and the Christian church was duped into believing a concocted story, when most of the 500 eye-witnesses were still alive? This has got to be the most outlandish theory ever concocted. Again, we see the sheer desperation behind this argument.
Let me give you a summary. Absolutely yes, you can trust the Bible. The utter weakness of these arguments, showing how desperate these critics are to discredit the Bible is evidence in themselves of the reliability of the Old and New Testaments. These are the very Word of God, passed on reliably through thousands of texts. You should not be intimidate by these weak and deceptive arguments.