There are a number of uncertainties and disputed issues in the early history of Islam.
Most of these disputes can be traced to Shi'a-Sunni disagreements. Shi'a often argue that history has been distorted to further a Banu Umayyad agenda. In many cases, complications with the historiography of early Islam have also resulted in lack of consensus within denominations of Islam.
Muhammad never told his followers who will succeed him, but people took from his interaction with Abu Bakr and his close relationship to be the next leader.
The uncertainties include: