Both the percent sign (and, by extension, the permil and permyraid sign) and fractions containing the number 0 are currently represented in the Minecraft font. However, while both contain circles, which are rendered about the same size in most supporting fonts, in the Minecraft font they appear different, which is an inconsistency and can cause confusion with nearby symbols such as apostrophes and commas. I'd recommending changing the percent sign and such to use the larger circle instead of the two pixel dot (may fix this and provide the resource pack).

To reproduce, paste %‰‱ ↉⅒ into chat and note that the circles in the first three symbols are shown differently from the zeroes in the last two.

Further notes

It may be advisable to re-assign the current symbols to the Arabic-Indic equivalent symbols for per hundred, thousand and ten thousand, as they do indeed use dots: ٪؉؊