The rule for critical hits states:
When you score a critical hit, you get to roll extra dice for the attack’s damage against the target. Roll all of the attack’s damage dice twice and add them together. Then add any relevant modifiers as normal. To speed up play, you can roll all the damage dice at once.
For example, if you score a critical hit with a dagger, roll 2d4 for the damage, rather than 1d4, and then add your relevant ability modifier. If the attack involves other damage dice, such as from the rogue’s Sneak Attack feature, you roll those dice twice as well.
So I would expect that, if a character were enlarged via the Enlarge/Reduce spell, they'd roll an extra 2d4 damage on a critical hit. The Reduce part of that spell states:
The target's weapons also shrink to match its new size. While these weapons are reduced, the target's attacks with them deal 1d4 less damage (this can't reduce the damage below 1).
Does that mean, though, that if they scored a critical hit while reduced in size by the same spell, they would roll 2d4 and subtract that value from the damage that is dealt?