Bugs happen, but it is always unfortunate when you run into one that blocks progression. Even temporarily. I am in general pretty averse to playing the same thing over, at least in story focused games.
I really like the mark system, I love being able to set up a bunch of orders ahead of time and then trigger them and see my whole group work as one. I kind of want to see it as a feature in other tactical games though I guess it only works if they are also real time.
I probably should try setting some up marks for weapon configurations and retreats too. It is good that you tend to have a quiet period before fights so you actually can take advantage of the mark system, setting it up during a fight seems like it is a path fraught with peril.