The word prehistoric refers to a time before a culture has written records. The word itself, therefore, points to the chief challenge in studying and understanding prehistoric cultures: they lack, by definition, any written accounts to help us understand their past.
As historians of ancient Roman history, such as Miranda Aldhouse-Green, have pointed out, we often have to rely on accounts of prehistoric cultures, such as the Druids in England, provided by cultures with writing, such as the Romans who conquered the the Druids. Because of this we are relying on another culture's interpretation of a prehistoric culture, which means the account can be filled with the biasses of the culture telling the story. Going back to the Druids, can we really trust what Julius Caesar has to say about them, given his own prejudices as a Roman?
Prehistoric cultures force historians to rely on artifacts, such as the remains of buildings, sculpture, artwork, clothing, tools, and weapons. These can yield quite a lot of information but also leave blank spaces that a written record could easily fill in. Therefore, historians have to often rely on speculation or educated guesses about how a prehistoric society functioned, worshipped, or traded.
Prehistoric societies are hard to study due to a shortage of written records. Even where written records are left, they are open to interpretation. Many of the records have been lost over thousands of years due to weathering and conquest. While historians know that ancient man used tools, historians often cannot piece together these tools or know exactly how they were used. Many times the bodies of ancient people are used for study, but there are ethical issues concerning disturbing ancient graves. It is hard to decide whether the wounds on an ancient corpse were caused in a sacrificial ritual or a war.
There are also issues with Carbon-14 dating. By measuring the amount of Carbon-14 left in an organism, anthropologists can tell its approximate age. However, this is not an exact number so it is hard to get an exact timeline for the events that happened in ancient times.
To add to readerofbooks' response, another challenge historians face when going past the earliest recorded histories is the complete and utter lack of written records.
Why is this such a problem? Historians cannot trace the languages used, the political and cultural norms, and the daily life movements of early people groups who pre-date, for example, the Sumerians and Akkadians of the Tigris-Euphrates River Valley. Likewise, although there is plenty of archaeological evidence concerning agriculture in the Andes mountains dating back nearly 15,000 years, historians are as baffled about the lives of early Andean people groups as they are about the first Andean languages. The best we can do is guess, unless something comes up that can give a historical account.
There are many challenges that historians face when they study the prehistoric era.
First, there is the issue of time. The further something is away from our time, the harder it is to study. There are no eye-witnesses or even second hand accounts. Moreover, there is also the possibility of distortion.
Second, when it comes to pre-history, the time distance is so far away that we cannot even meaningfully talk about history. Moreover, the very little data that we have has to be interpreted. And there is no telling whether our interpretation is correct or not. For instance, is an artifact a piece of garbage, something prized, a weapon, or something else? It is hard to say. This is why no two scholars agree.
Finally, there is always the bias of the one who studies.