This may be the same issue as https://bugs.mojang.com/browse/MC-153171 (currently closed).

Initial state:

• A Master Shepard villager with 'green dye' for 12
• Discounted trade to 11
• 64 Green dye
• Villager recently refreshed (audible indicator) and slept

Actions A:

• Open villager trading window
• click on green dye (64 green dye added to trading window)
• click on emerald (53 green dye remaining in trading window)
• click on green dye (25 green dye picked up)

Expected:

Only 11 dye used in trade.

Actions B:

• Open villager trading window
• click on green dye (64 green dye added to trading window)
• shift-click on emerald (1 emerald added to inventory, 28 green dye remaining in trade window)
•  click on green dye (28 picked up).

Expected:

5 emeralds added to inventory (up to limit) and 9 green dye left over.