According to the CNN article: "The government snooping continued into early this year, including a period when Manafort was known to talk to President Donald Trump."
So if they were wiretapping Manafort's phone, they wiretapped Trump as well.
Let me explain how wire tapping works. What you do is monitor the phone line of the person under surveillance. There is no need to monitor the phone lines of everyone who ever calls the suspect. It is true that, as a side effect of the wire tapping of the person under surveillance, you will be able to hear the conversations the suspect has with others. That does not mean that those other individuals' phones are being tapped.
There is no need to prove that everyone who might telephone the suspect is also part of the investigation in order to get permission to tap a phone line. Such a requirement would be absurd. Indeed, objecting to wire taps on anyone you might wish to telephone seems to me highly suspicious. Everyone is entitled to a reasonable degree of privacy but, if you happen to call someone who is the target of an FBI investigation, it is too bad if what you say to the suspect is monitored.