Zen practitioner and trainer here.
Proper meditation is a very powerful journey inside and has the power to uncover a lot of trauma or bad experiences masked or buried by other coping mechanisms. It can be said that purification is the process of uncovering these traumas and/or problems and solving them definitively, removing all secondary effects in the process, hence making person more free.
As OP said, the mechanisms are overly complex and extremely powerful. It's both not understood by modern science and very underrated by "woo woo" people.
Coming to your point, these breaks are caused by being faced with these traumas unprepared or without someone to support you. If you're advanced enough, you can face them yourself and solve them. If you're not and somehow face them, a more experienced practitioner can help you to collect yourself and face them at a later time. These experiences push you to the boundaries or out of your comfort zone, for sure.
In these cases, anxiety and other emotions are tip of the iceberg. If you're anxious about meditation, you wouldn't be able to focus properly.
In Zen, the practitioner wouldn't search for a root cause since it's not obvious. So, you don't try to process what's happening real time. These root cause reveals itself later. Either by noticing real-life changes or enlightenment (completion of background processing).
Hope that helps. If you have further questions, I'll try to answer.