The reason really varies from person to person. Some may find it difficult to understand the entities involved and their relationships. Whilst others may find it difficult to apply normalisation etc principles. So it can due to combination of one or more of the below
Difficulty in understanding business domain as well as the relationships between various business entities. This mostly happens at logical modelling phase
Applying different levels of normalisation for the tables to reduce redundancy of the model. This will happen during physical modelling phase.