Hmm, when testing I did come across a way to mess up the movement routes in the flashback scene - happens if you go through the text too quickly - but I did put some safety nets in there. Every character in that scene has 'through' on, so they can't get stuck. Did it happen in the flashback scene itself, or in the mountain pass?
And yes, it is 100% possible to get through the game without losing any allies!