It's not just >99.99 that is affected. *Every* bet is 0.005% harder to win than advertised. It's just that when the bet is advertised as 0.01%, the 0.005% error is half your advertised chance of winning, so it is hugely significant.
What this means is that on average 1 in every 20,000 bets in the history of the site was incorrectly marked as a loss instead of a win.
With 750 million bets on the site, that means that around 37500 bets were settled as losses when they should have been wins.
37500 bets assuming that every bet was made on the 10,000x multiplier.
No, you aren't understanding:
*Every* bet is 0.005% harder to win than advertised
Every bet was unfair, not only the 9,900x multiplier ones.
For example:
To win <49.5 you had to roll <49.495000 to beat the unfair rounding, and so only had a 49.495% chance of actually winning.
Similarly, to win >50.5 you had to roll >= 50.505000 to beat the unfair rounding.
Every bet on the site had a 0.005% smaller than advertised chance of winning.
That means that roughly 0.005% of all bets were unfairly paid as losses when they should have won.
Edit: Due to 0 working fine that means the expected number is actually ~4.
How was 0 working fine?
If you try to roll "<0.01", you had to get <0.005000 for the rounding to give you a 0.00. That again is a 1-in-20k chance.
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