I used to have the same. In my case, it got fixed when I bought a Stratocaster (from their Squire line, which are not that expensive) and started practicing with it, because I was determined to follow the Blues track on this website.
You see, the Strat has three pick-ups and not much space (for a newbie's eyes) between them, and since I was used to playing my accoustic pretty much anywhere around the hole, I wasn't that precise with my pick at first. I kept sticking it too far inside in between the strings and if I didn't play in a specific place, I would hit the pickups with the pick every time, it made me mad. The electric sounds just fine with much more subtle moves and slowly the Strat has more or less forced me to play at the right spot.
Anyway, when I pick up the acoustic now while watching tv or laying in bed, I just play correctly over the hole, just like that. Hope that helps. Good luck with your issue!