Over the last 2 weeks or so, I have been using GitHub issues notebooks intensively. Overall it's working very well. This is the collection of paper cut issues I ran into. The first three in the list are indeed my top three.

• I miss the run button when I try to click on it around 50% of the time. When you move your mouse very slowly in and out of the run button you can see where it changes and how that is misleading.
  
• When switching back and forth between different editors or windows I easily lose track of where the keyboard focus is inside a notebook. This is less of a problem when a cell editor has the focus but very much so when the cell has the focus. Try: Give a cell the focus, Cmd+Shift+F, Cmd+1. You see that the only indication is the change in upper and lower border.
  
• I often click into the cell status bar when trying to give focus to an editor or I try to delete the "empty" line in a cell by using arrow-down to get there.
  
• After I create a new cell with Cmd+Enter I try to change the cell language with "change language mode" in the command palette.
• Undo of markdown edits replay in the rendered markdown. I'd expect that the cell goes into edit mode and then performs the undo.
  
• The first diff in a notebook is not revealed when opening the diff editor. Since we don't have the minimap or show diffs in the scrollbar it looks like there are no diff. We should follow the model of text editors here.
  
• I've seen rare situations in which I had screen cheese, see Screen cheese in notebooks #108764.
• When I open a notebook diff editor with double-click and then open the notebook file that is being diffed using Cmd+P, the latter opens as json Open notebook when diff editor is open doesn't the file in notebook editor #110894.
• 🏃 Open a GH issues notebook with problems. Open the Problems view and click on a problem. A second editor opens.
• When trying to delete output, I was always first looking closer to the actual output rather than the cell toolbar Output actions closer to outputs container #110959
• 💪 I repeatedly tried to use Find to look for information in the outputs... Notebook: find doesn't search in output #94239
• I repeatedly tried to use ArrowDown to go from a cell editor to the output below.
  • We have enough context keys to allow such customization (see Notebook navigation flow #110962 (comment)) and we will continue discuss about the default navigation flow in that.
• 🏃 The GH issues notebook loses its keyboard focus when: 1) run a cell 2) Open an issue from output by clicking the link 3) Cmd-Tab to come back to the VS Code window -> no keyboard focus. You have to explicitly mouse click into the notebook to bring it back.