Perhaps the first sentence would have been better as: "There are two other Java features that can affect the flow of control: assertions and exceptions. However, they should never be used to expicitly control the flow of execution except in the ways that they are intended to be used. That is, to handle exceptional circumstances arising in your program."
Exceptions and assertions can be used for flow control, but should not be so used, at least not for flow control in normal program execution. Both are meant purely for flow control in abnormal program execution, in other words for error handling.