While using manuscripts, the historians face a number of difficulties.

1. Different interpretations: Manuscripts were written with hand and as a result there were small but significant difference between any two copies. The scribes who copied them introduced changes with their own interpretations.

2. Poor handwriting: As the Manuscripts were written with hand and as a result there were chances of errors while copying these scripts.

3. Copying errors: Copying scripts introduced changes which grew over the centuries. As a result historians have to read different manuscript versions of the same text to guess what the authors had originally written.

4. Confusion: Different versions of Manuscripts lead to the confusion and it becomes a challenge to decide the chronological order of their release.