It looks like your iterating over every line in your file. Then you are iterating over the fields separated by commas, and storing each value in the second argument to your array, before immediately overwriting it with the next value (not sure why you're doing that, but we'll move on).
If there is a new-line after then last line of the file, you will attempt to insert a row with index 17, which is impossible, because you only have 17 rows, and the first index is 0.
Let's walk through the steps for that last line.
InputLine2 will be set to a blank string InputLine2 = ""
The next line will evaluate to String[] InArray = new String[] { "" };
Finally, inside the for loop you will set junior [17][0] = "";
This will see the exception above.
You probably should use a list, rather than an array, then it won't matter how long the file is.
Why not something like this:
Scanner scanner = ....
Iterable iterable = () -> scanner; // convert to iterable
Stream stream = StreamSupport.stream(iterable.spliterator(), false);
String[][] data = stream.filter(s -> s != null && s.contains(","))
.map(s -> new String[] { s.substring(s.lastIndexOf(",")+1) })
.toArray();