Cryptomator has no limitations itself. But if you are using Windows WebDAV as Volume Type, you are affected by a Windows bug with webdav, that causes a limitation of the WebDAV Drive based on the capacity of your system drive.
Explained here:
And of course there may be limitations from the storage provider (size and file count)
Further more, Windows WebDAV can not handle files larger than 4GB
As you still have problems when coping folders, I would try with Dokany. You can switch back to WebDAV at any time.
I have no Idea what the reason for your problems could be, but I assume the file system driver is somehow involved.
Some more Infos to Dokany vs WebDAV: