Update TWiLight Menu++ and nds-bootstrap to the latest stable versions using Universal-Updater or by manually copying the latest files to your SD card.
To fix the issue, it helps to understand why your emulator or console is rejecting the file: The Dsi Binaries Are Missing Please Obtain A Clean Rom
Either disable DSi mode in the emulator settings or obtain a proper DSi-compatible ROM. Update TWiLight Menu++ and nds-bootstrap to the latest
Verify hardware compatibility
You will likely not notice a difference for standard 2D RPGs. The Dsi Binaries Are Missing Please Obtain A Clean Rom
Unlike standard DS games, DSi-mode games require these files for encryption, camera, audio, and other DSi features.
Older dumping methods or low-quality downloads from the internet may have missed these secondary binary sections, resulting in an "incomplete" file that lacks DSi-enhanced capabilities.