The problem is that these taxonomy terms are numbers, but when they are retrieved using the standard function get_terms to populate the dropdown options, they are evaluated as strings.
Although the number 10 comes after the number 9 the string "10" comes before the string "9".
The arguments for the get_terms function don't offer the ability to handle the terms as numbers rather than strings, hence there is no such option in the settings for a taxonomy search filter.
The way to avoid this problem is to use leading zeros in the slugs of the terms, and then order the terms by the slug.
So if you have a term "100" you would set its slug as "00100". Likewise, if you have a term "99" you would set its slug as "00099".
Ordering by slug as strings "00099" comes before "00100", which is what you want, and the dropdown will display the term names, so it will display 99 before 100.