Last year a local exchange send my btc order 2 times. And i was honest enough to pay them back. But they should work more carefully.
You are a good Samaritan then. Only two out of a hundred can do that. Exchanges should be more careful in transactions going in and out, that way this kind of thing will be averted.
Doing it through manual transaction is better if there is a lot of bugs to the system. They are thinking all of the things go smoothly but manual is better if you don't have a good system.
They must put the more effort for that, why they don't just try to do a little transaction to check how good their system before doin a transaction? that's weird.