indexOf returns -1, if it doesn't find the element in the container. You should use indexOf on each string word and not on the array words:

var words = ['hello', 'sunshine', 'apple', 'orange', 'pineapple'];

var wordsWithA = words.filter(function (word) {
  return word.indexOf('a') !== -1;
});

console.log(wordsWithA);

try

var words = ['hello', 'sunshine', 'apple', 'orange', 'pineapple'];
var wordsWithA = words.filter(function (word) {
  return word.indexOf('a') > -1;
  
});

String.prototype.indexOf(searchString, position) takes two arguments:

1. First is the substring that needs to be searched.
2. Second is an optional argument, that is the position from where the substring needs to be searched, the default value of which is 0.

And the method returns the index of the first occurrence of the searchString, if found, and returns -1 otherwise.

In your case you can omit the position argument and do it as follows:

const words = ["hello", "sunshine", "apple", "orange", "pineapple"],
  wordsWithA = words.filter((word) => word.indexOf("a") !== -1);

console.log(wordsWithA);