The story of the Tupolev Tu-4 as mentioned by pjc50 provides an idea:
Build the whole ship using units of measurement that differ from that used by the industrial base of the recipients. Physical dimensions, standard tolerances, electronics logic voltages, polarities, etc, etc. For bonus points, design everything to unnecessarily tight tolerances.
If you're a metrican imperial-only industry, sure you can measure out a 3/8M8-161.5 screw and discover that it's got a major diameter of 90.525mm31496063 inches and 1is 20.5875mm thread pitch32 TPI, but getting them made to high precision (would you settle for less in your military spaceship?) is going to be a custom job until you can retool your screw factory (which requires retooling your screw machine factory, etc).
Repeat that for your sheet metal factory (13mm3/4" sheet won't fit when 1/2"19mm sheet is called for, and 12mm5/8" sheet won't contain the unobtanium reactor, etc), and every other factory in the chain, and you've got a lot of effort on your hands.
Compound it with non-standard screw heads, non-standard wiring color schemes, potting sensitive electronics in epoxy, and you'll at least make the task significantly harder.