I eventually figured out how to fix this issue so here it is if you run into the same trouble:
*The problem seems to be related to maps that are removed from the mission after tasks are assigned to it.
*I am almost certain I manually deleted all the storyboard entries before removing the map itself but doing so, and not just letting the map deletion cover this, is still a good idea.
*The map where the problem began was a duplicated map (the return to space after the ground section is complete).
*When I tried re-creating the map by name (and I typed it in) this did not help but when I re-duplicated the map from the original (meaning the initial space map that the mission re-used) where the name was generated automatically, the problematic dialogues were returned to the storyboard where they could be removed manually. This time it seems to have taken.
Anyway, hope this helps anyone who also runs into this.