Eating a singular unstacked pufferfish does not inflict any debuffs on the player. (tested in singleplayer)
Based on 1.11 decompiled using MCP 9.35 rc1
The problem is that the stack size is decreased (net.minecraft.item.ItemFood.onItemUseFinish(ItemStack, World, EntityLivingBase)) before other methods are called, in particular net.minecraft.item.ItemFishFood.FishType.byItemStack(ItemStack) which calls the method net.minecraft.item.ItemStack.getItem() which returns air because the count is 0.
This is a general problem and affects multiple items. Luckily they don't call methods which require a valid item at the moment.