HashMap<String, Integer> wordToCount = new HashMap<>();
            for (String root : words) {
                if (!wordToCount.containsKey(root)) {
                    wordToCount.put(root, 0);
                }
                wordToCount.put(root, wordToCount.get(root) + 1);
            }

String[] words = new String[] { "Рыба", "Рыбаки", "1Рыба", "Два Гладиолуса", "Гладиолус" };
for (int i = 0; i < words.length; i++)
{
    for (int j = i + 1; j < words.length; j++)
    {
        if (words[i].length() < words[j].length())
        {
            if (words[j].contains(words[i]))
            {
                System.out.println(words[j] + " содержит " + words[i]);
            }
        }
        else
        {
            if (words[i].contains(words[j]))
            {
                System.out.println(words[i] + " содержит " + words[j]);
            }
        }
    }
}