I did some additional testing. I moved to the web version and had the same issue with a note I tried to delete previously. Deleting a different note worked fine. The strange thing was that when doing a previous query, previously deleted items still showed up. Clicking on them made them disappear. This behavior points to a delay in the sync or some cache issue. Cleaning the browser cache didn't solve it.
The next day, back in the app, there was no issue deleting notes until a certain point. The same problem appeared. I don't know whether the app uses a temporary memory, but if it doesn't, there looks to be a delay in the syncing, which causes a bug to appear.