Hopper clock using 2 hoppers duplicate items inside

For my map I use a simple hopper clock build with 2 hoppers facing each other and putting 1 item in one of them, so that they constantly move the item back and forth generating a pulse, which is used for a different circuit with command blocks. Sometimes the item inside the hopper will be duplicated after a while so there will be 2 items in the hoppers. Now there will always be a item in the hopper so it won't give out a pulse anymore, just an high signal. The clock won't work anymore. I've had this problem ever since using the 1.8 snapshots. Right now I'm in the latest version 14w11b.