I have noticed the same problem. I have a character with a +2 charisma mod that is proficient in persuasion. That means the minimum roll that character can make on persuasion is 1(roll of 1) + 2(charisma mod) + 2(proficiency mod) = 5, and yet I have managed to roll a 4 on persuasion when trying to convince the lady not to shoot the goblin in the cage with a crossbow.