The second Deku Stick upgrade in
OoT can also be missed.
Basically anytihng involing the Forest Stage can be missed.
Also no SheikahSage. I was able to give him the Bunny Hood BEFORE getting the Master Sword. Besides if he could only be given the mask by then, it would make the Deku Nut and Stick upgrades completely impossible, all thanks to that glitch.