the capacity warnings are during save, the letpath warning is during battle maybe alien turn.
There are a couple in the log file:
Building: building_amstorage capacity: 10000
B_UpdateBaseCapacities()... updated capacity of building_amstorage: 0
......warning: base 0 has a wrong capacities[4].cur (2645 instead of 2615)
...
...subsystem 'production' - saved 28 bytes
Warning: ufo 'craft_ufo_scout' stats -8 is smaller than 0
...subsystem 'aircraft' - saved 640 bytes
...
Volume changed from 0 to 0 for sound 'footsteps/flesh3' on channel 0
LET_PathMove: Warning: Actor positions doesn't match (origin grid: 122:103:0, le->pos: 123:103:0)
event(dispatching): EV_ENT_PERISH 19610520
event(dispatching): EV_ACTOR_APPEAR 19974D10
event(dispatching): EV_ACTOR_MOVE 19B8FB18
LE_PlaySoundFileAndParticleForSurface: volume 0.80
...
Volume changed from 0 to 0 for sound 'footsteps/flesh3' on channel 0
LET_PathMove: Warning: Actor positions doesn't match (origin grid: 126:103:0, le->pos: 125:104:0)
event(dispatching): EV_ACTOR_MOVE 19D9EC08
LE_PlaySoundFileAndParticleForSurface: volume 0.80
...
Volume changed from 0 to 0 for sound 'footsteps/flesh3' on channel 0
LET_PathMove: Warning: Actor positions doesn't match (origin grid: 125:106:0, le->pos: 125:108:0)
event(dispatching): EV_ACTOR_MOVE 19974D10
...
......warning: base 0 has a wrong capacities[4].cur (2645 instead of 2600)
...
......warning: base 0 has a wrong capacities[4].cur (4431 instead of 4375)
......warning: base 0 has a wrong capacities[8].cur (1 instead of 0)