Hey there!
I had a slight problem by the part where we “personalized” the crate. I grabbed the points with “G” and pulled them apart. But some times it seems I pulled a “hidden” point from behind the point I actually wanted to grab. Often times they were the points at the cut lines.
I then selected the whole object, pressed “M” and said merge by distance. Blender said that it removed around 203 verticals. After this is worked fine but I wonder where those verticals came from?
A common cause of people ending up with duplicate verts is starting to extrude and thinking they cancel it. it is possible even accidentally to Shift D duplicate more geometry than you realise is selected.
What you have discovered actually is the way to investigate mesh problems, grab a vert and test move it to see if there is another hiding below it! Merge can miss some if they are not extremely close.
As NP5 explained. The extrude command ‘e’ hot-key, expects you to move the object immediately. Press ESC-key to cancel, cancels only the move part, but the extrusion (the copy) is still there. Hence double vertices.
Ah, I see! Thank you both! I guess I have used extrude then by accident while getting to know the hotkeys. 
It’s good to know that the copy still exists after canceling the extrude. Thanks 
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