For example, Hipchat's settings overlay (https://i.imgur.com/V3UOyMI.png) which should:
• Be a separate window
• Be sized properly for its contents instead of having to scroll
• Use tabs along the top for the settings categories
• Not have clipped left edges on all of the checkboxes
• Put the close button in the top left corner of the window like the rest of the OS
Compare to settings in Textual, which is an actual native application: https://i.imgur.com/5GFURBk.png
Beyond the design aspects, there's also the issue of performance (the OS's UI layout system is well optimized for doing UI layout) and battery impact.
The average "Energy Impact" of Hipchat as measured by Activity Monitor is 24x as high as Textual's. Twenty four! That puts it in 3rd place, beaten only by Google Chrome and Spotify (which IIRC is a similar "wrapped our webapp in CEF or electron). Hipchat does a bit more than Textual (inline image display), but not enough to justify its abuse of my battery life.
Aside from that, non-native applications inevitably introduce accessibility issues and UX incongruencies with the rest of the system that are difficult if not impossible to resolve entirely. There's a huge trade off made when using web tech for desktop applications and developers would do well to deeply consider their choice of technologies before acting.
You'll lose literally hours of battery life simply by running Atom instead of Sublime. It's absurd how little regard Electron devs are showing for end-user resources.