I agree with @skeggley, likely SHB larvae. You can filter them out if you wish. If you search the forum, you will find that you are not the only one, and I believe that Cedar wrote some advice somewhere on what to do about it.
Edit - Found the post I was thinking of:
http://forum.honeyflow.com/t/shb-larvae-in-the-honey-harvest/9729/5?u=dawn_sd