It's popular in some agile circles to question everything. This begs the question - is there any governance process in place? No? Then you're pretty much free to do whatever you want with the money provided to you to build software. If there is a Governance process in place, then that means there are decision rights in place as well. This decision rights almost always belong to the people providing the money for you to do your work.
Questioning those governance processes and questioning the principles, processes, and procedure that implement the governance processes usually starts with the owners of the governance process. If there is a mechanism for assessing the efficacy of the governance, that's where the questioning starts. Go find that place, put in your suggestions for improvement, become engaged with the Decision Rights Owners and then provide your input.
Standing outside the governance process shouting challenge everything is tilting at windmills.
So when you hear that phrase, ask do you have the right to challenge the governance process?