User interactions in recommender systems are inherently complex, often involving behaviors that go beyond simple acceptance or rejection. One particularly common behavior is hesitation, where users deliberate over recommended items, signaling uncertainty. Our large-scale surveys, with 6,644 and 3,864 responses respectively, confirm that hesitation is not only widespread but also has a profound impact on user experiences. When users spend additional time engaging with content they are ultimately uninterested in, this can lead to negative emotions, a phenomenon we term as tolerance. The surveys reveal that such tolerance behaviors often arise after hesitation and can erode trust, satisfaction, and long-term loyalty to the platform. For instance, a click might reflect a need for more information rather than genuine interest, and prolonged exposure to unsuitable content amplifies frustration. This misalignment between user intent and system interpretation introduces noise into recommendation training, resulting in suggestions that increase uncertainty and disengagement. To address these issues, we identified signals indicative of tolerance behavior and analyzed datasets from both e-commerce and short-video platforms. The analysis shows a strong correlation between increased tolerance behavior and decreased user activity. We integrated these insights into the training process of a recommender system for a major short-video platform. Results from four independent online A/B experiments demonstrated significant improvements in user retention, achieved with minimal additional computational costs. These findings underscore the importance of recognizing hesitation as a ubiquitous user behavior and addressing tolerance to enhance satisfaction, build trust, and sustain long-term engagement in recommender systems.