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Traditional single-factor authentication possesses several critical security vulnerabilities due to single-point failure feature. Multi-factor authentication (MFA), intends to enhance security by providing additional verification steps. However, in practical deployment, users often experience dissatisfaction while using MFA, which leads to non-adoption. In order to understand the current design and usability issues with MFA, we analyze aggregated user generated comments (N = 12,500) about application-based MFA tools from major distributors, such as, Amazon, Google Play, Apple App Store, and others. While some users acknowledge the security benefits of MFA, majority of them still faced problems with initial configuration, system design understanding, limited device compatibility, and risk trade-offs leading to non-adoption of MFA. Based on these results, we provide actionable recommendations in technological design, initial training, and risk communication to improve the adoption and user experience of MFA.