I'm working on a version of wormhole-based FTL travel, and one of the side effects of passing through the wormhole is going to be instantaneous heating of every molecule of the thing passing through. The heating works by dumping a specific amount of thermal energy into every molecule of the object passing through the wormhole, and the rise in temperature is thus affected by the specific heat capacity of each molecule.
In a previous question I asked about the maximum amount, starting from normal body temperature, that one can suddenly heat a human's entire body by. It turned out to be rather small, not much more than 1°C above normal. We can do a bit better than that by giving people mild hypothermia beforehand, so we're going to say that, as we can safely send humans through it, this wormhole raises the temperature of human flesh by about 4°C. This means that it dumps about 14 kJ/(kg*°C) of thermal energy into everything that passes through it.
This means that some substances which have much lower specific heat capacities would be heated by a substantial amount. The air in the spacecraft, for example, would be heated by about 14°C. Copper wiring would go up by over 36°C. Any spacecraft parts made of Tungsten would go up by almost 105°C. These temperature increases could cause the spacecraft to begin to leak or cause other dangerous situations. So, what major issues would there be with suddenly dumping 14kJ of heat into every kilogram of a spacecraft?
To clarify, the spacecraft in question is specially designed for this type of transition. The question is asking what would have to be designed differently and what could still go wrong.