I've been running VF3 on an iPad throughout development, and I don't have issues with being able to dig up the minerals. However, I think VF3 is a little bit fussier than VF2 when it comes to dropping peeps on various areas of the game (and especially collectibles).

Some tips that might help you...

• Make sure that you hold the peep over the collectible until the message "sees the collectible" is displayed, then drop the peep on the collectible
• Don't have the display zoomed all the way out (very small), since that can make picking up weeds and collectibles difficult