If you're wanting to build a muscular physique, then you need to lift heavy weights, and sometimes it doesn't matter if it's a machine or free weights. Some machines aren't that well designed, so you might not be hitting the muscle as well as you could, so yeah, that's the time to opt for the free weights. However, I personally use a mixture, and some of the guys I follow use machines regularly, and they have awesome physiques.
I do think it comes down to mindset a lot of the time. Machines have had a slightly bad reputation in the weight room over the years, and it's lead to a lot of 'gym rats' hating them and giving them that bad rep. Some machines can be very good at isolating a specific muscle group. Take the leg extension for example. Some people will say it's no where near as good as squats, but squats can also be fairly dangerous if you're lifting just that little too much weight, or if you don't know how to squat properly. As I've said, I've seen some of the biggest names in the business use that leg extension machine, so if it's so bad, why would those guys with amazing physiques use it??
I honestly think that some peoples opinions on this topic is like the debate in the Fast and Furious movies between the late Paul Walker and Vin Diesel - muscle cars vs imports - both have positives and negatives, but they both work in their own right - it comes down to personal opinion.
Machines are great for beginners. They allow the user to familiarise themselves with the feeling of contracting a specific muscle group, which then they will know what to feel for when switching to free weights. That is one of the biggest problems with free weights - people not quite knowing how to do it as they don't know what they should be feeling.
My advice? use both and see what you prefer! Sometimes the free weights won't always be available and you'll have to use the machines anyway!
Lee Gregory Fitness