Pick block on a banner gives an item with id tag in BlockEntityTag in its nbt data. Creating a banner with the loom also give a banner with id tag in BlockEntityTag in its nbt data. Mining the banner gives an item without the id tag in BlockEntityTag in its nbt data. This results in two stacks of the effectively same banner when picking block on a banner while you have the banner in your inventory.

Code Analysis

The loot table of banners only copy the patterns tag

while pick block uses

BlockItem.setBlockEntityNbt()

which adds the id tag to BlockEntityTag

Suggested Fix

Add

{
    "op": "replace",
    "source": "id",
    "target": "BlockEntityTag.id"
}, 

to "ops" as seen here