There's a huge difference between being skeptical and being self-deprecating. By all means one should play devil's advocate to their own impulses, but without practicing self-awareness, it's exceptionally difficult to come up with useful criticism of one's own thoughts and to unravel the complex interplay between thoughts, behaviours, and emotions. Because of this, many people give themselves poor/irrelevant feedback and form habits of thought that cause the same kind of negative self-evaluation to recur.
In addition, it's common for people to feel a sense of threat from their own negative thoughts, and the sympathetic nervous system doesn't very effectively differentiate psychological threats from physical. Subsequently, attacking oneself can lead to fight-or-flight response, which can cause a cascade of changes throughout the body, including the brain, which can manifest as cognitive biases, for instance attentional bias towards negative stimuli or interpreting ambiguous stimuli to be negative.
Hopefully you can see how the combination of these effects could create a negative feedback loop, causing typically rational skeptic to veer off into unfounded, inconsistent thoughts blaming oneself and generating further negative emotion.
So ultimately, I'd agree with you 100%, there's a line to be drawn. The unfortunate thing is that it's very fuzzy from within one's own mind to discern where that line should be drawn, and negative feedback loops can set up instability that overshoots that line, even when meaning well. For individuals with this kind of pathological negative self-examination, framing things positively can have a huge impact on how they are actually perceived and acted upon. And for people struggling with depression/anxiety, it can make a world of difference in outcome to simply reframe a thought like: "I should have worked harder on that work deadline. Now everyone hates me because I missed it and I'm going to get fired." as "I'll feel better about my work and my relationships with colleagues if I give myself extra time and raise concerns early about deadlines."
At the same time, an excess of positive thinking can absolutely create it's own share of psychological effects and reactionary feedback loops. For example, in bipolar disorder we see a grandiosity of thought and excess of confidence that leads to underestimating risks and inflated expectations, which collide with reality (often disastrously) leading to a large down swing in emotion, and the resulting post-manic depression.