This issue applies to the current test version (1.04.347661) as shown here:
As I have mentioned in a previous post, the game allows players to build customized versions of prototype ships like the Praxis. Players can then queue-up as many of these customized versions in as many of their shipyards as they want. Once the first ship is finished, you can no longer queue-up any more of that ship, but the ones that are already queued-up will be finished. This allows players to build very powerful fleets early in the game and, I believe, violates the principle of only getting one of each prototype ship. To fix this, you need to not allow prototype ships to appear in the list of available designs that you can customize. The first screen snapshot below shows that the Praxis is available for me to customize. In fact, it appears in the list twice for some unknown reason.
A second related issue is that, if you create a customized variation of a prototype ship like the Praxis in one game, that customized variation will appear in subsequent games as soon as the base prototype ship becomes available, regardless of whether or not the player has researched all of the technologies necessary to use the items that make-up the customized variation. The second screen snapshot below shows that the Praxis and the variations that I created in previous games are now available for me to produce. The third screen snapshot shows that the best missile weapon that I can add to a design is the Avenger, but it also shows that the design already has Photonic Warheads. I find it difficult to believe that this is the way you want this to work. Again, this issue goes away if you just do not allow prototype ships to be customized.
I have saved a copy of my current game that you can use to see what I am talking about to DropBox at the following location: