Are refunds ever made in multiple payments? I received an electronic deposit, but only for about 2/3 of the my refund amount.

No, you should not expect to receive multiple deposits from the same tax agency (you should expect one deposit from Federal and one from your State if you filed a state return). Please see this helpful FAQ for common reasons why the refund you received is lower than you expected: https://ttlc.intuit.com/replies/3288510