How did the Council of Nicea get such a bad rap? I’ve heard countless arguments from Atheists and Muslims that the 1st Council of Nicea banned books from the Bible, hid inconvenient truths, expunged Mohammed from the Bible and so on, we know that the council was dealing with the Arian heresy, so how did the Council get such a bad rap?
The council has a bad rap because a lot of people think the Bishops bowed to the secular power of Constantine whose judgement and wisdom is always likened to the secular authority of the day.  So when Trump was president, it seems like Constantine is just making baseless decisions on no facts, now that Biden is president people will view Constantine as evolving Catholic doctrine.
However, this is what happened:

The Council was opened by Constantine with the greatest solemnity. The emperor waited until all the bishops had taken their seats before making his entry. He was clad in gold and covered with precious stones in the fashion of an Oriental sovereign. A chair of gold had been made ready for him, and when he had taken his place the bishops seated themselves. After he had been addressed in a hurried allocution, the emperor made an address in Latin, expressing his will that religious peace should be re-established. He had opened the session as honorary president, and he had assisted at the subsequent sessions, but the direction of the theological discussions was abandoned, as was fitting, to the ecclesiastical leaders of the council. The actual president seems to have been Hosius of Cordova, assisted by the pope's legates, Victor and Vincentius.


St. Athanasius assures us that the activities of the Council were nowise hampered by Constantine's presence.


https://www.newadvent.org/cathen/11044a.htm

The purpose of the Council of Nicea was to ensure that the Two Natures of Christ, fully God and fully man would be enshrined in Catholic doctrine and Arius would be anathematized.  It's no surprise then that groups who think that this is not correct doctrine (Jehovah's Witness and Islamic doctrine is closely linked to Arianism) would be more than willing to criticize the council and a favorite whipping boy of those who criticize the council is Constantine.  It's hard to criticize Athanasius, except for being a little blunt, but his writings are so like Luther's that I don't think Protestants bother to come down too hard on him.
But the council didn't ban any books, except the musings of Arius, I believe that was the Council of Rome in 382, and banning the parts of the Gospel talking about Mohammed would need more details to understand, I'm guessing someone says there is some sort of prophecy that Jesus laid out that there would be yet another prophet?   I'd never heard of that before and it certainly has nothing to do with the Council of Nicea.