Shift-clicking an item into the GUI of the IBC will duplicate it and will appear in the IBC but not be taken from player inventory.
I have InventoryProfilesNext installed which may also be a culprit in this case, i will report more as i test further!

This works with buckets but also tanks from other mods like mekanism ultimate fluid tank

Before click:

Shift + Left-Click

This bug has been fixed in 71bec7c.

Thank you for your report!

In order to verify this issue, I implemented some fluid container items in HaC and confirmed its operation, but no dupe occurred.
I have temporarily commented out at 059f499 the feature to address the issue, so this issue will probably be removed in the next update.