In the recent years, studies of design and programming practices in mobile development are gaining more attention from researchers. Several such empirical studies used Android applications (paid, free, and open source) to analyze factors such as size, quality, dependencies, reuse, and cloning. Most of the studies use executable files of the apps (APK files), instead of source code because of availability issues (most of free apps available at the Android official market are not open-source, but still can be downloaded and analyzed in APK format). However, using only APK files in empirical studies comes with some threats to the validity of the results.In this paper, we analyze some of these pertinent threats. In particular, we analyzed the impact of third-party libraries and code obfuscation practices on estimating the amount of reuse by class cloning in Android apps. When including and excluding third-party libraries from the analysis, we found statistically significant differences in the amount of class cloning 24,379 free Android apps. Also, we found some evidence that obfuscation is responsible for increasing a number of false positives when detecting class clones. Finally, based on our findings, we provide a list of actionable guidelines for mining and analyzing large repositories of Android applications and minimizing these threats to validity.