This is a huge question, but the short answer is that it would be difficult to find two types of religion more destined to clash (here, I will be lumping together all the Native American religions with the broadest strokes for the purposes of discussion, which is not to minimize...
their nuance and individuality).
First, Native American religious practice was joined with everyday life: there was no separation of the sacred and the secular. In Christianity, there is a divide between the sacred and the secular, with specific times and places of worship that exist apart from everyday life. This led to confusion for the Native Americans, especially since most of the land they lived on was considered sacred space. Where they farmed was sacred, for example, and they rejected the European concept that this could be taken from them or swapped out with some other piece of land. The colonists and missionaries, for their part, couldn't understand that seemingly secular practices, such as dances, were sacred to the Native Americans. To the missionaries, the Native Americans could seem like irreligious heathen because of their merging of secular and sacred.
Further, some of the symbols that tribes worshipped, such as snakes, were traditionally considered Satanic by the Christians, and so some tribes were wrongly labelled devil worshippers.
In addition, many tribes practiced henotheism, meaning they believed that different gods protected different territories. This led them to embrace polytheism, or the idea that there is more than one god. The Christians strictly rejected polytheism. Native Americans could not understand why the Christian God and other gods couldn't coexist, while the Christians were bent on converting the natives and eradicating what they thought were their false gods or idols. Christian exclusivity thus clashed with Native American inclusivity.
These religious differences needed much space for talk and a context of mutual respect for the different cultures to stand a chance of understanding one another, but that kind of dialogue was in very short supply.