I've noticed a whole lot of things in Innsmouth where order is pretty unclear. I believe the last I heard was that if there was a timing dispute, the first player decides.
The Ancient One is at 1 doom in final combat, all investigators including Tommy Muldoon (who removes a doom, among other things, when devourered), are devourered (say, by Glaaki). Who wins?
There are 5 elder signs on the board. A 'gate block' adds the last uprising token to the track, but is also the 5th 'block' for Mandy's mission. AO woken up or no?
Scenario 2 actually happened to us, we played it that the investigators won.