I shall give you an example
The answer to 6a parses as "Analysis" - but the answer to 3d is "Tonic"
The 7th letter of analysis is an "I" but this has to go in the grid where the T of Tonic is, therefore there is a "clash". You now have to decide whether to put an I or a T there. Unfortunately for you both "analysts" and "ionic" are words and so you can't tell that way. When you solve 16/17 it becomes obvious what "the clash" is.
In this one example the answers are "analysts" and "tonic"