Some problems that I've noted with GEDCOM are:

• Not all family files support all types of information provided for in the GEDCOM specification, and, especially in the early years of GEDCOM, the specification may not provide for all types of information that some family files allow;
• The relationship between items of information in the GEDCOM specification may not conform to or accomodate the relationships between those items in the family file. (For example, the GEDCOM specification defines parent-child relationships through the Family or Marriage record, whereas in the FHS family file there is no direct association of parent-child relationships with marriage or family records.)
• The GEDCOM specification, during the years that it has been under development, has changed in ways that make earlier GEDCOM files non-conformant with later specifications
• Some specifications are so broad that the programming required to interpret the information can become quite complicated.