Scene slides appearing horizontally, as triggers to move forward are within the masterslide

You could go apply a swipe trigger to the slide to create the link at the slide level so you can see the slides vertically. Then turn them off when you publish.

• Go into Story View and select all the slides.
• Then go to slide properties on the right side and deselect the prev/next buttons but select the swipe options.

Thanks for the reply Tom. So is it recommended that we don't use navigation triggers on the master slides?

What you see in Story View is merely thumbnails for your convenience. It has no connection to what the learner sees. 

What the learner sees is controlled by the triggers.

Some people cannot overcome their OCD enough to live with that. If you can, you don’t need to make any changes.

There is no recommendation about putting triggers on masters, except for creating the effect you need for the learners.

What Walt said. :)

The Story View is a quick way to see the flow of the slides. Since you have triggers on the master there is no "visible" connection between slides. By adding the swipe to the slides you can see the connections. But if you don't need to, then you don't need to do anything.