I searched on the forums for an answer to my problem and none of them worked for me but i found my own way to resolve my issue.
I happen to have a few email accounts but i only use the main iCloud account for my notes.
When i updated my phone, the update turned on the notes on all my email accounts which made my notes search facility stop working.
I turned off the notes on all the accounts and this fixed my issue.
This is on macbook pro and iPhone 6.
I hope this helps someone
MacBook
Pro, OS X El Capitan (10.11.4)