It is very easy to accidentally disable keyboard shortcuts.
First of all, I have to say that the function to disable keyboard shortcuts is not very common and not obvious. I'm not familiar with any other program that supports disabling shortcuts. I think disabling shortcuts is a great feature, however, most Gnome users are not aware of this option. At the same time, the design of the GUI of the Shortcuts tab in Preferences makes it very easy to inadvertently disable the keyboard shortcuts. Then, for users who do not expect such a feature, it is difficult to understand why the keyboard shortcuts stopped working. There is a checkbox to disable/enable shortcuts, but most Gnome users, unaware of this option, ignore the presence of the checkbox. Many users leave the Preferences window with Shortcuts tab open as a quick guide. I am attaching a screenshot with the highlighted zone.
Any click in this zone changes the value of the checkbox. When moving the Preferences screen around the screen, it is very possible to click in the highlighted area. Although all shortcuts appear dimmed in the shortcut pane when shortcuts are disabled, it's very easy to miss this point when moving the window. I suggest changing the GUI design in one of two ways. 1st option is to minimize the clickable area by making the click acceptable only around the actual checkbox control. The 2nd option is to highlight an area that can be clicked when the mouse is over it. Gnome Terminal already uses such controls, I've attached other screenshots.