I don't know of a foolproof way, but I think it's a matter of awareness, recognition, and discovery.
First, you need to be aware: not only do phrasal verbs exist, but they are also rather common. If you read (or listen to) English long enough, you're going to come across them.
Second, you need to recognize their format (generally: verb + preposition, although sometimes verb + adverb).
Armed with this information, when trying to interpret a sentence or imperative (such as, "Come on!"), you need to say to yourself: "Wait! Maybe this is another one of those pesky phrasal verbs..."
Sure enough, when you look it up in a dictionary, there it is:
come on (phrasal verb) used for telling someone to hurry ⇒ Come on! We're going to be late.
(Many good online dictionaries will give phrasal verbs their own entry.)
So, as you try to learn the meaning of certain sentences, remember: not all words should be examined individually.
My daughter was going out with Ted. Evidently, they broke up about a week ago, but I didn't find out until yesterday, when I dropped her off at school.
Can you find the phrasal verbs in those two sentences? There are four of them.