For example: I was grabbing a lot of stacks of dirt. I searched for dirt and started shift+clicking them into my inventory. When I was done I had been given a stack of diamonds and a stack of coralium.

Are you sorting based on quantity in the grid? If the dirt quantity gets lower, the dirt will shift to the right, which causes you to pick other items. In that case, this is not a bug.

No, I always sort by name for that very reason actually.

Then this probably due to lag.