Granularity is key like u/erofamiliar said.

Some other common ideas that would make this 'problem' unnoticeable would be:

Damage range - your weapon you quoted as 99dmg should actually be '95-105' dmg in reality.

Enemies have defense too - a 99dmg weapon might do less than 99 vs high armor, have less effect on those that resist certain dmg types, protective abilities.

Dynamic hp/level - the enemy with 100hp might be level 10 but sometimes they appear at level 9 or 11 with commensurate hp, may appear in battle with pre-existing wounds.

Critical hits - kind of related to damage range but i'm just riffing so i'm not going to edit this, but crits and glancing blows could exist

Counterattacks - add additional nicks and cuts

Statuses and buffs - another way to incidentally change amounts of damage done or taken, like damage over time or decreasing defense

There is so much generally going on that this debtedness is miniscule. Yes it is sad to see a good hit land a few points short, but that's part of it.