The SO post linked by the OP indicates that in that specific instance, there were some misspelled keys in the manifest (plist) file, so you could check that.
We have not had any problems with new installs on iOS 9. We have had problems with updating apps as described below.
When iOS 8 came out, there was a bug that prevented updating Enterprise apps OTA if things occured in the following order:
Device has iOS 7.
Install Enterprise app OTA.
Install iOS 8.
Try to update Enterprise app OTA.
The workaround was to put a different bundle identifier in the manifest (plist) file, e.g. add "-iOS8" at the end and using that manifest file to update an app on iOS 8. The bug was fixed in a later version of iOS 8, but I don't remember which one.
With iOS 9, the bundle identifier in the manifest file must match the bundle identifier of the app in the .ipa file (at least in part becuase of the "Masque Attack" scenario). So now, in the following scenario:
Device had iOS 7.
Install Enterprise app OTA.
Installed iOS 8.
Update Enterprise app OTA with different bundle identifier in plist.
Installed iOS 9.
Try to update Enterprise app OTA.
On some of our devices, the last step fails. Actually, it may not be exactly that set of steps. Some of the devices may have had iOS 8 for the initial install of the app, which used the different bundle identifier. The symptom was that if we used the correct bundle identifier in the manifest file, the Install pop-up never even appeared, and if we used the modified bundle identifier, the Install pop-up appeared but the app didn't actually install (or maybe it was the other way around). I don't remember what showed up in the device console output, and I didn't save it anyhere. In any case, for devices that ended up in this state, the only way we could get the app updated OTA on iOS 9 was to delete the app and install it again with the correct bundle identifier in the manfiest file.
However, as I mentioned, we have not had any problems with new installs on iOS 9.