Salesforce custom report types have several limitations:
Object References Limit: Maximum of 60 unique objects per custom report type.
Fields Limit: Maximum of 1000 fields per report type layout.
Data Capture Limit: Reports capture up to 2,000 rows in a formatted report, with export limits of 100,000 rows and 100 columns in XLSX format.
Customization Constraints: Limited flexibility in modifying field names and default fields.
Setup Complexity: Requires admin access and can be complex for inexperienced users.
Reporting Functionality Limitations: Limited customization options and challenges integrating external data sources.