No you were right, I had the same issue, but not every time. I have done some tests and it seems that Ren'Py still allow to click on a "room trigger" during the animation as if you were on the "map of the ship" screen. Maybe a problem of layer persistence.
This is how I triggered the bug : at night coming from one sector to another (let's call them sector 1 and sector 2), on the "map of the ship" screen, I clicked "forward". The "gate" animation to sector 2 launches with its sound. If I click during the animation on a place which had a "room trigger" back on the "map of the ship" screen, the sound turns to the "room I clicked" screen one's, and when the animation ended, I'm not on the "map of the ship" (that normally crossfade from "sector 1 color 1 night" to "sector 2 color 2 early"), but instead I'm on the "room I clicked" screen and still "sector 1 night", so when I click "forward" again it launches the "gate" animation to sector 2 again.
Hope you can understand what I mean
Xavster, if you need more infos I will try to tell despite my bad English.