You are using your already rounded value to calculate splitSeconds.
What you want is the difference between timer and timerSec.
Assuming timer is a float measuring seconds this should work:
var fractions: int = 100; // for hundredths of sec
var timerSec: int = Mathf.RoundToInt(timer);
var splitSeconds: int = Mathf.RoundToInt((timer - timerSec) * fractions);
alertTimer = String.Format ("{0:00}:{0:00}", timerSec, splitSeconds);