I used the mods.harvestfestival method to implement 2 new items for the general store.
(mods.harvestfestival.Shops.addPurchasable("harvestfestival:general", minecraft:egg, 50);
mods.harvestfestival.Shops.addPurchasable("harvestfestival:general", minecraft:apple, 25);)

As soon as i use /mt reload there will be a warning, that these items have been registered again with a different id and after that they will be doubled in the shop.
Jaredlll08 commented, that this problem is on your side and he has nothing to do with it.

latest.log:
latest_client.log:
used Forge-version: forge-12.18.2.2106
used Crafttweakerversion CraftTweaker_1.10.2-3.0.12

Partially probably, but he should probably fix that thing where apply gets called multiple times when it shouldn't too