Hmm - this issue is not, in fact, confined to Experimental: the problem is with the "hull and hold" system of ships. Because each "hold" of a ship is defined as a separate vehicle, if one adds a great many holds, the game takes the whole convoy (ship with holds) as needing more than one tile of a stop, or else all the cargo will not unload. It is possible to reduce the length of these "holds" to zero, but then the icons for the various different types of holds are all stacked on top of each other and impossible to discern clearly.
There is, however, an easy if not entirely ideal workaround for this issue: for stops on inland waterways (this issue will not affect docks on the open sea), add an extra tile to the stop to make it longer, in the same manner as with a railway platform. This will allow all the goods to unload.
I am not sure whether, strictly, this counts as a pakset bug or a design issue, but I should be interested in the views of the developers of the Standard version of this pakset what best to do about this issue.
