Why does Scene 3 insist on showing up as Scene 4 in Scene 3s place?

Story View is programmed to represent the overall flow of a Storyline course. With a linear course, that's easy. When there's branching, it can get trickier. It interprets how scenes are interconnected. It might even be impacted by when and how inter-scene links are added. 

Yes, it can be frustrating if it doesn't match how you would diagram the scenes. Fortunately, it doesn't impact how the course runs for the user. 

How are you triggering the items to jump to the Scenes from the first Slide?  Are those triggers on Layers?

You can also check how your buttons appear top to bottom in the timeline.  The scene connected to the button on the bottom of the timeline will always be on the far right. The scene connected to the button on the top will be on the left, etc.

If you reorder the stacking of the buttons . . . save . . .close and reopen Storyline, then it should reorder the scenes for you.

CJLu​: This isn't about the Story View issue, but there is something that might simplify your programming.

You wrote:

I am using hotspots over images with states.

It sounds like the user needs to choose from among separate images.

If that's the case, why use hotspots at all? The action(s) that happen when the user clicks a hotspot (for example, jumping to a scene) could be triggered to run when the user clicks the image. That would let you take advantage of the automatic functionality that comes with using built-in states, such as the image automatically changing to the Selected state when clicked. And, if only one should be selected, you could put them in a button set. Or an image could automatically change to the Visited state.

Even if you don't need that automatic functionality, you'll still have fewer objects to deal with if they user can just click an image instead of a hotspot over an image.

For reference: 

• PRIMER: Take advantage of built-in states | E-Learning Heroes

• https://www.articulatesupport.com/article/Storyline-360-Working-with-Button-Sets 

• PRIMER: Hotspots vs. Transparent Shapes | E-Learning Heroes (This is about using transparent shapes instead of hotspots, such as when multiple click areas need to be over a single image. It's just another option to consider.)

It looks like with yesterday's update the timeline now will work the oppostie of what I stated earlier.  The top item in the timeline will put the triggered scene to the far right and the bottom item will place it on the far left.