Responses

I dont think so. The main reason was, 001 was ordered to kill civilians but he didn't, he declined an order. As punishment, the heads was gonna take out some of the numbers for 001s insubordination (punish the team for the leaders sin) but instead 001 betrayed them and tried to leave and so on (mind you, Jin wqs about 13/14 at this time too). The flashback was cut up multiple ways so I can't remember the exact chapters, but I think this was it
I can't remember if this happened but wasn't the reason 001 was being chased 'cuz he was ordered to kill the numbers 'cuz they were no longer needed? And that he didn't do it, so the camp labeled him as a traitor thus what lead to the chase which 003 made even more complicated by killing the numbers? Does that chapter exist?
Also just to confirm... The main numbers doesn't know that order yet right? I mean the real reason why 001 was chased by 003 and the other numbers