The "Violations" panel is a list of anywhere the currently loaded codebase violates the spec. The line items are actually the parent items that contain violations. If you click on an item in the list, the relevant parent will be expanded to show its children and any violations.

There are 2 distinct kinds of violations:

The values in the "#" column are the summed up violation metrics for the given parent.

Tip:

You can easily add a violating item (a red cell) to the spec by clicking the "Add to spec" command on the context menu. This will change its color from red to the default color, and remove the violation. You should then consider where the new item should be positioned relative to its siblings, and drag it to its new location if needed.