FWIW, I was curious (since I use that too) and the "logistic cargo wagon" mod makes a direct copy of the standard cargo wagon. It does not change, in any way, the number of inventory slots in the wagon.
So if you previously had a different number of slots, I'd guess another mod changed the number of slots on the core wagon (or all wagons) and so logistic cargo wagon picked that up.
The copy is made in the data.lua
phase, so it is entirely possible the other mod randomly loads after, not before, LCW now. or something mutates it in data-updates or data-final-fixes.
Anyway, point is: not a Krastorio ... anything. Possibly an LCW bug, not creating their cargo-wagon clone late enough, possibly not a bug at all. YMMV.