https://fallout.fandom.com/wiki/Director%27s_recordings

The Institute was in favour of the CPG, though not super direct with their involvement, but two things went wrong.

One was that the Commonwealth was divided, a lot of the elements of the CPG didn't like each other, and needed little prompting to get into arguments or open conflict.

Two was that an Institute department head sent an experimental synth to a meeting with the CPG against the orders of the director at the time. The synth malfunctioned and killed all the other representatives, presumably after some sort of argument triggered it's combat protocols.

Upon discovering one of the delegates was a synth, and with everyone who had been in the room dead, the CPG fractured completely. Some blamed the Institute, some blamed other settlements, some blamed both. The Institute found no one was willing to talk to them anymore and basically decided that diplomacy with the surface was a dead end at that point and decided to focus on their strained infrastructure and assassinating people who tried to rile the commonwealth up into trying to attack them.