If everything is subsonic, designed properly, it’s all stable. If everything is supersonic, and you designed properly (which is different than subsonic), it’s all stable.
While you’re in the middle though, you have portions that are subsonic and portions that are supersonic, which means you have shockwaves all over the place that tend to cause flow to separate and reattach as the shockwaves move around, which causes loads on the vehicle to constantly shift, leading to instability. If the lighting is right you can actually see the shockwave on the upper aft surface of the wing on some commercial jets moving around, but it’s so localized and designed for that it’s a non-issue.
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