Static analysis frameworks (SAFs) such as Soot and WALA have been a fundamental support in today’s software analysis. They usually adopt various analysis techniques to transform programs into different representations which imply specific properties, e.g., call graph can demonstrate the calling relationships between methods in a program, and users rely on these program representations for further analysis like vulnerability detection and privacy leakage recognition. Hence, providing proper program representation is essential for SAFs. We conducted a systematic empirical study on program representation faults of static analysis frameworks. In our study, we first collect 141 issues from four popular SAFs and summarize their root causes, symptoms, and fix strategies, and reveal nine findings and some implications to avoid and detect program representation faults. Additionally, we implemented an automated testing framework named SAScope based on the metamorphic and differential testing motivated by findings and implications. Overall, SAScope can detect 19 program representation faults where 6 of them have been confirmed or fixed, demonstrating its effectiveness.