I can see two possible reasons for this:

A) your Bluetooth settings got corrupted. 
B) the Harmony Hub doesn't attempt pairing long enough.

Solution 1 for A: Resetting Bluetooth settings 
1) Delete the Bluetooth settings files by entering this into Terminal.app: 
sudo rm /Library/Preferences/com.apple.Bluetooth.*.plist 
sudo rm ~/Library/Preferences/ByHost/com.apple.Bluetooth.*.plist 
2) Reboot 
3) Retry pairing.

If pairing still does not work, Bluetooth may need a more thorough reset:

Solution 2 for A: Resetting Bluetooth settings and hardware 
1) Delete the Bluetooth settings files by entering this into Terminal.app: 
sudo rm /Library/Preferences/com.apple.Bluetooth.*.plist 
sudo rm ~/Library/Preferences/ByHost/com.apple.Bluetooth.*.plist

2) Hold down Shift+Alt while clicking on the Bluetooth icon in the menu bar. This gives you an entry called "Debug". Inside the "Debug" menu, choose "Remove all devices", then "Reset the Bluetooth module".

3) Reboot.

4) Retry pairing.

At this point, pairing should work. If it still does not, you may have stumbled over an issue I've run into myself recently, which brings me to…

Solution for B: 
With the latest version of the Harmony App for iOS, I noticed that the Harmony Hub only briefly attempts pairing when it brings up the screen and will attempt to only once – even if you go back and forth to/from the previous step.

The solution there is to open Setup Wizard in Remote Buddy and have it look for devices already before the Harmony App gets to the Pairing step.

Once that step has arrived and a few seconds have passed, the only way I found (during setting up a new PS3 Remote device) to get another chance for pairing was to delete the device and create it anew.

I hope this bug in the Harmony app/hub will be be addressed by Logitech with a future release.

If possible, please let me know if the above helped you resolve the issue.

Cheers, 
Felix