File Parsing in Java Using Collection
Your code looks overly complex to me, using three different collections when one, the hash map, would be enough. Use your code from the wordList loop when emptying the scanner, and update the word count there:

while (scanner.hasNext()) {
    String word = scanner.next()
    Integer count = wordCount.get(word)
    wordCount.put(word, count == null ? 1 : ++count)
}