I think I remember this from 9398 and 42030. This example is from 42069.

To prevent misplacing other pins.

Yup.. Lego do this in a lot of sets - even more so with ones for younger kids..

(recently seen with the Friends' Ski Lift set

if you fill the hole with a small, cheap part.. then it eliminates making an alignment mistake later on

 

which means less support calls "Little Jimmy is having trouble building this set"...   so adding in a half-pin, could be saving them a tonne of money with support! :)

I always thought it would be parts for the B-model, but I guess it does make sense to prevent pin misplacement.

Also the same reason that creator and other sets use oddball colours in the internal structure... less likely to get things wrong

I understand. I guess... By that system there would be a lot more halfpins in models. There is a lot of holes to wrongly fill. I suppose these are critical, but then again there are more critical connections than these...

Still, I'll consider this explanation as the final one and go on building!

They are also sometimes (not in those cases) used to keep the axles from slipping. I used them to keep the 4L With Stop used as a front wheel axle from slipping and getting "loose". I honestly though, during the build process, that those two in 42069 will also be used as a slip-preventive measure.

When I built the crowkillers Scorpion, it used 1/2 pins in the end holes of 9L liftarms that operated the changeover catches. When I asked why he did that, he said it was just in case people didn't follow the instructions and used the last hole instead of the 8th hole and have to tear the model apart to fix it.