How do I stop ships from auto moving to a particular location

This looks to me like one of those things that often happen during the design phase of any program, missing a requirement simply because it never occurred to the designers that it might be needed. What is needed is an option in the govern -> ships -> going ... -> should go to column that assigns no goto target to the ships selected in the "going to" column. The same is true for govern -> ships -> of type.

Without this, the only way to turn off the autopilot of all ships is to select them one at a time and right click on the ship (which unassigns the ships destination) or select a new target destination by right clicking the mouse on another tile. If you only have a few ships you want to do this with it isn't too bad, but if you have a lot of them it can become next to impossible and extremely tedious (not fun).

Select the shipyard that is building the ships, click on the Rallypoint button (bottom right on the shipyard info panel in the main view) and select Nothing.