This can happen when transform inheritance is disabled. Check out the front-foot-tip and rear-foot-tip bones in the spineboy-pro project. They have inherit rotation and reflection disabled:
Loading Image
When you scale the root bone to scaleX -1 to flip the skeleton, those two bones don't inherit the reflection (they don't flip over, they continue pointing the same direction).
At runtime you can use Skeleton scaleX and scaleY to flip the skeleton, including bones that have transform inheritance disabled. In the editor I'm afraid there isn't such a feature yet, so if you need to flip your skeletons during animations, you would need to either avoid disabling transform inheritance or fix it up by manually flipping the bones that didn't flip, eg by setting their scaleX to -1.
Disabling transform inheritance can be quite useful and is a feature not commonly seen in other software. That is likely because it creates more cases for how transforms are applied, which is already pretty tricky and has to work in all scenarios, no matter how unlikely.
