I've noticed this bug specifically with the picture-in-picture mode. But the steps to recreate are pretty simple.
1. Begin watching Crunchyroll video in iOS app
2. Place app into picture-in-picture mode (usually by tapping the home button, in my case)
3. Allow video to run to completion
4. Return to app (usually by pressing the full screen button in the picture-in-picture window)
5. App closes the video and sends you to your queue
Now, here we can note that the app thinks that you have completed the video and shows you a progress bar to say as much. However, if you quit out of the app and reopen it or look at your queue on a computer, the progress will not be reported, and both will act as if you never watched the episode.