Apple uses the ".icloud" extension to indicate that files are not yet downloaded to your Mac, but available through iCloud Drive. Finder automatically downloads these files on-demand when you double-click to open.
iOS handles this in a different way, so files are automatically downloaded on demand and you never see the ".icloud" extension.
If you sync folders through iCloud Drive and a 3rd-party sync solution (e.g. Dropbox) at the same time, it can happen that the 3rd-party solution syncs the ".icloud" files, without downloading the actual files from iCloud.
Then, you might see ".icloud" files on iPad or iPhone on these 3rd-party storage providers. The 3rd-party storage providers will not know how to resolved these files to your actual files.
Solution: Uncheck the Optimize Mac Storage Checkbox (Settings -> Apple ID). Then wait until iCloud resolves all files and the 3rd-party sync solution syncs these files.
In general, it is not advisable to have folders synced by more than one services, as it can lead to bugs like this one. Ensure your synced folder is not on the Desktop or Documents, as these are folders synced by default. We recommend to change the folders in this case, so each services syncs its own folder.
If you have ".icloud" files but deleted the original file on iCloud Drive, the file is gone and can no longer be retrieved.