For some reason after working with a shape for a little while, the transform the points (corners, edges, whatever) get out of alignment. Notice below in the rectangle in the middle.
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This is more of a comment and a wild guess, but since I needed to add pictures, here it is.
Did you check if you have "Align to pixel grid" turned on? It might be if you created an RGB document, since it is part of the default options for RGB documents.
To check, select a shape and open the Transform panel (Shift+F8). Check if "Align to pixel grid" is ticked.
If you don't see this option, then you might need to open the extended options. To do this, click on the right top corner of the Transform panel and select "Show Options".
If the option is ticked, then the shape vertices will align to exact pixels when you start working with them.
To turn the option on for just one shape, then just select the shape and tick off the option. You can also select several shapes and tick this option off for all of them at the same time.
To turn this option off for all future objects, then click on the top right corner again to show the options menu and tick off "Align new objects to pixel grid".