I do not understand your first question. What exactly is not happening; is the train not going into the loading state; is cargo not boarding it (despite being on the station), is the train not leaving the loading state, or do you mean something else entirely?
As to the second question, infrastructure renewal is automatic, but can be overridden manually. Ways will eventually wear out with the passage of time and vehicles. If the player takes no action, these will renew automatically (at cost) when they are worn out, unless the player has insufficient money, in which case they will degrade and eventually become impassible.
However, upgrading can be altered manually. Hold down shift when dragging a way over another way and, instead of replacing that way instantly, the new way type will instead replace the old way type when it comes time for renewal. This allows for cost-efficient upgrading.
Similarly, one can shift+drag the way removal tool over the way, which will disable upgrading, causing the way to degrade when it is worn out.
Renewing a way manually (i.e. by dragging a new way over it without holding shift) will reset the way's wear to zero again.
