The Bedwars Resource HUD doesn't properly account for the "Punch to deposit" feature.
For example, punching the ender chest with 5 iron ingots in hand reduces the iron ingot count by 5.
A way to check for this might be to use the chat message:
§r§7You deposited x5 §r§fIron Ingot §r§7into your §r§dEnder Chest§r§7!§r