Here you have a song where you can see the use of wish. Wish + past tense
The prologue to the musical "Into the Woods" also has a lot of examples of how to use "wish". You can try to write down what each character wishes for. You will probably recognize them, as they all come from traditional fairy tales.
And if you watch the whole musical, you'll realize that wishing sometimes you have to be careful what you wish for...
Phrasal verbs in English are very, very common. The best advice is to calm down and pick them up just like any other verb, one at a time.
Also, a good idea is to pay attention to them when they turn up in songs. Lindsay Dow has a fantastic Youtube playlist with songs that use them. Check them out!