Sometimes an Item's NBT data will be mixed up and permanently prevent it from stacking to items of the same Type and NBT.
For Example:
Item's NBT before issue: 
item_name{display:{Name:'

{"text":"Dragon Scale","color":"green","italic":false}

'}}

Item's NBT after issue:
item_name{display:{Name:'

{"text":"Dragon Scale","italic":false",color":"green"}

'}}

This causes them to be considered different items due to the Order at which the NBT is presented in the game.
it happens randomly to items that are being given through /give commands as well as when you attempt to quick transfer between chest and inventory using ShiftClick.

I have tested the following things which conclude that Spigot/Bukkit is the issue....

• Issue does not occur on Vanilla Server of exact same world files/items.
• Issue does not occur on Vanilla Local worlds with same world files/items.
• Issue is only reproducible when playing the world on either a Bukkit or Spigot server jar.

Useful Information:

• I do not use plugins of any kind.
• Items that are affected are ANY/ONLY items that have NBT data for Name/Custom Tags/Lore etc.
• Consistently attempting to stack the stack glitched items can sometimes cause them to Duplicate.
• Issue occurs regardless of Item being involved.