What is the difference of a Cryptomator vault to a VeraCrypt container?

Cryptomator is a client-side encryption solution which is optimized for the use of cloud storage.

When using VeraCrypt or other container-based encryption solutions, all files you store in a container are bundled within one single large file. The cloud does not handle such files very well. A small change can cause the full file to be reuploaded into the cloud. In addition, if multiple persons work with the same files at the same time, conflicts are not detected on a per-file basis but you get a copy of the container file. Using the files from a mobile device is more or less impossible because you would have to download the full container file first.

When using Cryptomator, each file is encrypted individually. A change to a file causes only this file to be reuploaded. In addition, Cryptomator has integrated conflict detection and handling. This allows efficient use of cloud storage and mobile access to your encrypted data. Of course, individual encryption of each file also means that Cryptomator can not hide all information. Especially, file dates and sizes are still visible. Details about Cryptomator’s security target are described here.