I have noticed something like this - the core ships you start the game with, flagship, colonizer, maybe miner too, when you try to design to upgrade them in the shipyard _sometimes_ the modules etc take up less space in the initial version, so when you remove them you can not even immediately add them back in in the existing space.

I kind of never liked that you started with ships you could not actually build anyhow (for instance nobody starts being able to produce a survey module, yet every empire has one on their flagship). I would prefer a check box option to have all races start with no ships in the game.