Cydia Substrate 0.9.6000 has made massive internal changes to be compatible with the latest jailbreak for iOS 9 from Pangu.
0.9.6010 fixes the 32-bit armv7 slice, which was keeping extensions from loading into Cydia. (Note that, additionally, all 32-bit binaries, in particular extensions, must be recompiled using -Wl,-segalign,4000 for iOS 9 due to a change made by Apple. Extensions that have not been recompiled might "get lucky" and work, but they will usually either fail or even crash.)
0.9.6011 fixes an issue in 0.9.6xxx where it no longer worked on iOS versions before 5.0.
0.9.6100 blocks extensions on iOS 9 that are guaranteed to crash some key processes (such as Cydia), will inject into too many processes (due to a mismatched filter), or which will lead to subtle bugs (by invalidating the codesign of the target process). This new version also fixes some issues developers were seeing attempting to hook functions in particularly well-sandboxed processes, and adds support for the latest version of Cycript (which now runs Substrate as an injection vector).
0.9.6101 fixes an issue where Cycript could not inject into a 32-bit process. (This bug might have affected Substrate in some more general way? I am not yet sure about this.)
0.9.6110 fixes an issue where extension that are corrupt (often on purpose by the developer for obfuscation purposes :/) cause Substrate's attempt to detect whether the extension will cause the process to crash to actually just cause Substrate to crash :/. (In addition to all of the usual numerous improvements I make every time I cut a new release.)