Grounding requirements for main panel and subpanel
The NEC only requires two ground rods if one doesn't suffice the 25ohms requirement.  If an additional ground is installed then a minium of 6' spacing is required between them.  The only time the neutrals and grounds are allowed to tie together are in the main disconnect. 
To keep the neutrals and grounds separated, a 4 wire should have been used to feed your sub panel.