You need to look closely at your code and consider carefully what you are doing. Your code in no way matches up with your description.

1. You say you skip words less than 3 chars, but your code contains tests for <3 and <5, and the code path for >4 seems identical to that for 3 & 4.
2. You split the first phrase into words, but not the second.

   And you then test if each word in the first phrase contains the whole of the second phrase.

3. You have a whole bunch of else { next; } clauses.

   Do you realise that if you omitted those clauses, it would just loop to the next iteration anyway?

   So what is their purpose?

The bottom line is, with the disparity between your written description and you code, and a bunch of redundant stuff in your code, I cannot work out what you are actually trying to achieve, so I cannot really suggest anything.

First decide and write down what you actually want to do; then try to write code that matches that description; and then, if it doesn't do what you want, come back and ask again.