Yes, to a point. An itinerary builder can check the plan you have put together and flag the obvious clashes, such as a hotel whose last night ends before the return flight departs, a gap where the traveller has no accommodation at all, or two hotel stays in different cities on the same night. It can also show you when a transfer or activity has been placed on a date that falls outside the stay. These checks come from the dates and times already sitting in the itinerary, so they work on any trip you build in the system.
What it cannot do is judge whether the plan is realistic. If a flight lands late in the evening and you have put a morning tour the next day in a town some hours away, the system has no way of knowing how long that road journey really takes, so it will not stop you. The same applies to visa processing time, minimum connection time on separately booked flights, and local closing days for attractions. Those still need your own knowledge of the destination.
How much warning you get also depends on where the parts of the trip came from. Items booked through a connected supplier arrive with proper dates and times, so they can be checked properly. Items you have typed in yourself, such as a local guide or a train you arranged offline, are only as accurate as what you entered, and a missing time means nothing to compare against.
When you set up your itinerary builder, go through one of your more complicated past trips in it and see which clashes it actually picks up, so you know what you still have to check by eye before the plan goes to the customer.