I have an iPad Air 2 and had a similar issue after upgrading to IOS 9. I found a solution with the help of Apple Support:
Issue is that the new NOTES program is having an issue with some data in your existing notes and is therefore not showing all the formatting options.
Resolution Steps:
1) Backed up ipad to my PC via iTunes
2) Signed-in to iCloud.com and copied all my notes to MS Word
3) Deleted all notes from NOTES in iCloud.com
4) On iPad, went into Settings/Icloud and turned off NOTES in icloud
5) On Ipad, went into Settings/General/Reset and did "Reset all Settings"
6) Manually re-keyed notes from MS Word back into Notes in icloud.com. I did not copy n paste for fear I might also copy whatever data is causing the issue to begin with.
7) On iPad, signed back into icloud and then turned on Notes (in icloud).
8) My notes appeared on my device with with all formatting options present. ISSUE RESOLVED.
Then had to re-enter my various settings and logins for my apps and accounts on the device. Didnt take too long.…