If you pass a Date object to the parse() method of DateJS, it will return the object (link), and the addDate() method also does not create a new object (link). So while you created a new theDate object for every b value, you modified the same object in the while loop, and put references to it into the master array.

The solution is to create a new Date object every time you modify theDate. For example, change this line:

theDate = Date.parse(theDate).addDays(1)

...to this:

theDate = new Date(theDate.valueOf()).addDays(1)

...or this (DateJS defines a clone() method):

theDate = theDate.clone().addDays(1)

This will clone the theDate object before adding 1 day to it.

Not sure why you need that library, this snippet does the job:

const errorFunction = () => {
  const days = [1, 2];
  const i = [0, 1];
  const today = new Date();
  const addDays = (date, numDays = 1) =>
    new Date(new Date().setDate(date.getDate() + numDays));
  return days.reduce((acc, day) => {
    return [...acc, ...i.map(item => [day, item, addDays(today, day)])];
  }, []);
};

console.log(errorFunction());

Let me know if this is what you are expecting.

As @kol pointed out that I was putting references in the Array.

So instead of a reference, I did this :

function errorFunction() {
  let master = []

  let a = [1,2] //a simple array to loop over

  a.forEach(function(b) {
    let theDate = Date.today() // 8th Sep 2021
    let i = 0
    while (i<2) {
      theDate = Date.parse(theDate).addDays(1)
      Logger.log(theDate) // dates are alternating between 9th and 10th september
      master.push([b,i,new Date(theDate)])

      i = i+1
    }

  })
  
  Logger.log(master) // all dates are 10th september
}