Free weights load the body through space and demand stabilisation, while machines fix the path and load one muscle more consistently.
For hypertrophy the difference is small. Studies comparing matched programs find similar growth, because the muscle responds to tension and effort regardless of what supplies the resistance.
The differences that do matter are practical. Free weights carry over better to standing tasks and sport, train stabilisers, and scale in small increments. Machines are easier to learn, safer to take to failure without a spotter, keep tension more even through the range, and let a client train around an injury by removing the joint that hurts from the equation.
Most good programs use both: free weights for the main lifts, machines for the accessory volume that would otherwise be limited by fatigue and technique.