It isn't a bug. If the software were to ensure when you rounded up that it didn't exceed a specific amount, then it wouldn't technically be rounding. If you think about it, when you round UP you're saying (for example), "I want this prize to be 10% of the pot, unless 10% isn't evenly divisible by X, in which case I want it to be MORE than 10% of the pot". By definition you are going to exceed the pot if your prizes are rounded this way, unless they all happen to be evenly divisible by X.
The "Leftover" is meant to divide up any leftover pot - and nothing more. If your prizes exceed the pot amount, there isn't anything left over, thus nothing left to distribute to make sure the pot is entirely awarded.
The workaround for this is to set your prizes to round down, and assign the leftover to one or more of the prizes. Then the prize total won't exceed the pot amount, and all of the pot will be allocated.