When using multiple devices, it may happen that encrypted files are not synchronized correctly between devices.
Cryptomator for Desktop just performs encryption, synchronization is handled by the cloud providers app which must be installed too. On the other hand the apps for Android and iOS access the files in the cloud directly. Sychronization problems can just not happen there because the files displayed in the app are actually already written to the cloud.
Thus, the reason for synchronization problems is not Cryptomator itself. Most of the time it is some problem in the cloud providers app or app configuration.
What you can do
Check if non encrypted files are synchronized correctly. You may place a new file in the cloud or modify an existing one. You can also place a testfile next to the file masterkey.cryptomator and see if this one is synchronized. To check if the files are synchronized you may either navigate to the synchronized directory on another desktop computer, look at the files through the online interface of your cloud provider or use the “Add existing vault” feature from within the apps, which will display existing non masterkey-files.
If regular files are not synchronized you may contact your cloud provider for support on how to fix synchronization issues. Sometimes restarting the synchronization app from your cloud provider or removing the connection to your cloud (logging out) and synchronizing all files again solves the problems.
If those regular files are synchronized, but your encryped files are not this maybe something else. You can run Sanitizer on the vault to check for errors like unresolved synchronization conflicts. Those may happen when two clients write to a file simultaneously. Normally Cryptomator for Desktop resolves such problems but if not, Sanitizer can detect them.