Lost a gallon of beer on my first dry hop because of that.
My solution is to only use pellets for dry hopping, cold crash if possible, and tie a sanitized nylon hop bag over the end of the siphon tube that goes into the bottling bucket. Don't snug it right to the end of the hose, tie the end just over the hose so you have a big baggy hanging off the tube. I lightly cinch a 1/2" stainless hose clamp on the end to help with holding the hop bag on and weighing it down into the bucket. Leave the end of the siphon alone. The siphon will definitely clog less with careful racking and the bag will catch any straggling pieces that make it through.
"This song goes out to me because I'm so f*ckin' cool!"~John Reis