"In phase" means "at the same place in some cycle." So here it doesn't mean that the people don't work together or don't work well together. It means that their levels of understanding and abilities rarely match. Some are always more advanced than others, but that may change over time. The ones behind might catch up and then be ahead. Other examples: The economic recovery in Europe is not in phase with the U.S. Over the last two years, inventory buildup has not been in phase with sales.

'in phase' Here is meant that the works do not act together for example - 'those people are not in phase with those people' But in the context of the book it probably means by 'in phase' as these people do not work together.

It is when waveforms or patterns line up together in frequency (are synchronized) to produce resonance. It is saying that knowledge workers do not work well together ("are not on the same page" is another expression), because each one works based on new, specialized, timely knowledge that each other one does not share. At least, that's how I interpret it.