I think the intention is that the -ve score is applied for combats that are to come. So that when you cross out the last unmarked box you suffer -1 die on all combats from there on until you cross out the last -1 box. From which point you take a stun marker and suffer -2 for the next combats etc. This means the value in the last box has a purpose (or in the example of the Crocodile, the last 3 boxes).
It is the -ve score in the next box that applies rather than the one you just crossed out.
But I may well be wrong.....
I do have a follow on question about this though:
If you cause enough hits to pass straight from uninjured to -3, do you take stun counters for -1 and -2? (and in so doing suffer the automatic loss for the 2nd counter at the same time?)