In the MCU Scarlet Witch has been portrayed as all-powerful and indestructible. She single-handedly tore through the Multiverse, wielded the Darkhold, dreamwalked through universes, destroyed the Kamar-Taj and killed the Illuminati. She killed Black Bolt, the Inhuman King, within seconds by rewriting reality and erasing his mouth. Wanda then murdered Captain America and Captain Marvel without even breaking a sweat. However, she is not without weaknesses and can be put in disadvantageous positions. So let us explore some of her weaknesses.
It’s common knowledge by now that Wanda has severe mental health issues. She definitely has PTSD. After all, her parents died right in front of her when she was just a child, eventually, she lost her brother as well and then had to kill the love of her life to try and save the planet just to see him die all over again at the hands of Thanos. So yeah she has issues. While in the MCU, these mental breakdowns have led to her unleashing her power and using her grief to further it. This was seen during Avengers: Age of Ultron when she felt Pietro die and during WandaVision when she ended up creating the hex. But these breakdowns make her careless and reckless. Her raw strength may increase but she loses all her tactical skills and strategies. This makes her defense extremely weak and unreliable.
While Wanda is immensely powerful and can use chaos magic to defeat her opponents, she is only human. Her body has physical limitations and is only as durable as a human body can be. Her use of magic also drains her physically and is quite exhausting for her as is seen during Multiverse of Madness. She is vulnerable to all attacks and bullets and was easily injured by Proxima Midnight during the attack on Vision. She was also taken out by Hawkeye during Age of Ultron when she attempted to brainwash him.
Scarlet Witch can also be overpowered by constant attacks at her which would prevent her from casting a spell as that requires time and patience. Thor used this idea during Uncanny Avengers #4. However, she did manage to eventually take out Thor from the battlefield. This fact can be exploited by her enemies although it won’t give them too much of an advantage.
This is a weakness that stops Wanda from expanding her Hex without any limits. Her hex-casting has a range and it is limited by her line of sight. Moreover, her hex-casting ability is also very unpredictable. This is pretty obvious when she simply did not realize that she created the hex over Westview. She also did not have a whole lot of control over the hex. However, in the comics, over time she becomes much better at controlling and casting the spell.
Chaos Magic is inherently unpredictable in nature and simply cannot be tamed. It is a power only possessed by the prophesied Scarlet Witch. And often this unreliability backfires as her spell fails. Sometimes her spells have gone extremely awry and out of hand. This happened during the storyline of House of M where one of her spells inadvertently created a monstrous being who was born with every other mutant’s lost powers. Her powers related to Chaos Magic need to be harnessed and polished. This means that she needs to spend time learning and mastering the spells. That’s exactly why she needed to train herself using the Darkhold after WandaVision and before Multiverse of Madness.
This is arguably one of her biggest weaknesses that can be exploited by enemies. Wanda is a glass canon which basically means that she has a great offence but struggles at defense. If there was some sort of a sneak attack planned that she had not foreseen, its likely that she would fall victim to it. That’s exactly why Proxima Midnight and Corvus Glaive managed to overwhelm her and vision with their surprise appearance. This means that someone like Bullseye or The Punisher could successfully snipe her from a distance.