Intermodal transportation development today is often a matter of public-private partnerships, where Government (probably State and Federal when you’re talking about international ports) primarily invests tax dollars to get private businesses to develop and, depending, manage the different modes involved.
So yeah, ultimately these problems are a result of Government shortsightedness, incompetence, corruption, and maybe even deliberately letting the “fruit rot on the vine” to further certain goals we wouldn’t be willing to accept if done openly - and it’s completely “bipartisan.”