$ file app
app: Mach-O universal binary with 2 architectures
app (for architecture i386): Mach-O executable i386
app (for architecture x86_64): Mach-O 64-bit executa
Unfortunately, the non-Apple version of GNU gdb is currently unable to debug universal (or 'fat') binaries (ones that contain both 32-bit and 64-bit executables).
One option is to use lipo
to extract a single architecture and run gdb on that:
lipo -thin x86_64 -output app-x86_64 ./app
or
lipo -thin i386 -output app-i386 ./app
If you'd prefer to debug the combined executable, you could try using LLDB, or an Apple version of gdb.