A workaround for the correct values. Force the train to refit to some other cargo, that is not available on both stations, and back to the required cargo on loading. You will get capacity to be recalculated on refit and always get the right values and graphics.

Capacity CB code
https://dev.openttdcoop.org/projects/xussrset/repository/entry/src/freight/cargoes-capacity-refit.pnml
Loading speed CB code
https://dev.openttdcoop.org/projects/xussrset/repository/entry/src/freight/cargoes-loadspeed.pnml
Graphics code
https://dev.openttdcoop.org/projects/xussrset/repository/entry/src/freight/cargoes8/container/containers.pnml

Typical code to choose - (random_bits >> 1) & 0x01

switch (FEAT_TRAINS, SELF, cargo8_container_2_20or40_sprites, (random_bits >> 1) & 0x01)
{
0: cargo8_container_40_sprites;
cargo8_container_2_20_sprites;
}

A workaround does not work for long train. last wagons of 9 square train become damaged the same way - capacity does not fit the random bits

To prevent error I've commented the difference in capacity CB.
If you would like to test you have to uncomment these strings:
switch (FEAT_TRAINS, SELF, container_20and40_cargo_capacity,
[ STORE_TEMP(2, 7),
((random_bits >> 1) & 0x01) ] )
{
// 0: container_2040_cargo_capacity;
container_2_20_cargo_capacity;
}

switch (FEAT_TRAINS, SELF, container_2_20or40_cargo_capacity,
[ STORE_TEMP(2, 7),
((random_bits >> 1) & 0x01) ] )
{
// 1: container_2_20_cargo_capacity;
container_40_cargo_capacity;
}

I think the problem here is that the game doesn't like to change the cargo capacity of vehicles when they are not in the depot. This is because is can cause desyncs and is unreliable in certain situations (giving the vehicle more cargo that it can actually take). This is seen if a NewGRF which has been adjusted to give a vehicle in the game a different capacity. This gives an error saying "vehicle xx has had capacity changed. This can harm the game state" or something along those lines.
I would not consider this a bug, rather the approach of your NewGRF may need a different approach to the issue.

The game already allows changing capacity at station with autorefit (outside depot!).
The problem is that it does not force recalculating capacity before loading (after autorefit and new cargo trigger) .

This issue has been automatically marked as stale because it has not had any activity in the last two months.
If you believe the issue is still relevant, please test on the latest nightly and report back.
It will be closed if no further activity occurs within 7 days.
Thank you for your contributions.

The problem is not fixed in master 27012019

Hmm, the trigger is called after the cargo quantity is reserved, as well.

I might be 100% wrong, but this issue reminds me of autorefit bugs I saw when testing cdist stuff for fonsinchen, which resulted in this fix f790d70#diff-ebbc445f07842947d83d0f98b7fa5140L1568

The comment is interesting, curious if cargo loading reservation causes the autorefit to not happen.

https://yadi.sk/d/NdfWgDWMlMD2BA
https://yadi.sk/d/3uZONAAy_1RSvg

This issue has been automatically marked as stale because it has not had any activity in the last two months.
If you believe the issue is still relevant, please test on the latest nightly and report back.
It will be closed if no further activity occurs within 7 days.
Thank you for your contributions.