Some older emulators (like DeSmuME versions before 2015) or cheap R4 clones do not properly support DSi-enhanced ROMs. They try to parse the ROM header, see the DSi flag, look for binaries, fail, and throw this error instead of falling back to DS mode.
Download the DSi BIOS and firmware files from your real DSi. Then, use only verified “No-Intro” ROM sets. The No-Intro project ensures every ROM is a clean, verified, 1:1 cartridge dump, DSi binaries included. If a No-Intro ROM still gives the error, the game was never DSi-enhanced to begin with—so force DS mode. Some older emulators (like DeSmuME versions before 2015)