This is basically the challenge of playing Settlers 2, to have a well functioning transport
Even with the best planning, this tends to happen. Following tips may help:
1) change transport priorities. You want stuff off the roads. If wood/stone has high prio
but your roads are full of food, nothing will be transported. Put food higher.
2) make parallel roads and cut the clogged road in the middle. Because it has dead ends, it
will slowly clean up
3) stop production of redundant materials. Example food: stop production of foodstuff.
Whatever is on the road will get away.
4) In crisis, remove a flag. All stuff on that flag will be gone. Depending on the product,
that might not be an issue. Food is essentially free, gold coins, not so much.