Also just bought this and also very excited to try it out--but I think I found one more inconsistency. The resistance/weakness sidebar on p. 55 says you decrease or increase damage by two boxes, but the rules breakdown on p. 353 says one box (which also seems to jive with the fact that the general description of damage says a 'more effective Damage Type' increases the damage by one box, and the fact that reducing damage by 2 boxes would basically mean resistance for hazards is the same as immunity, since PCs can't really get above 2 damage except with massive impact)
Yes, this is something we realised we'd missed after printing, unfortunately - two rules from two different stages of the game's playtesting phases. For the best experience, treat resistances on hazarda as decreasing the marks they take by one, and resistances on CHARACTERS as decreasing the marks by two. This relfects that, as you say, it's difficult for characters to deal more than one or two marks of damage, but hazards can throw that out far more easily.
It'll be corrected in PDF next time we do a release, and in print if we ever get the chance to do a version two :)