Morgana is vulnerable against invisible/teleporting burst champions as she can shield and bind/ult those she can see coming at her but she's still a little squishy. Watch your cooldowns, keep up control wards, and be quick on the Zhonya's. Keep in mind that your ult provides true sight so can help against those invisible/duplicate champions.
Champions that summon minions that can get in the way of her bind are also a hindrance. Luckily, most of them are AP champions so throw up a shield and find a way around those pests.