1. 'Damage Control' skill, 'Autonomous Systems' perk: the 50% crew loss reduction is actually affecting overload duration; stacks in a multiplicative manner with the actual reduced overload duration effect.
2. 'Flux Modulation' skill, 'Advanced Routing Algorithms' perk: 'unapply' effect is linked to getEmpDamageTakenMult(), rather than getPhaseCloakUpkeepCostBonus().
Same skill, reduced shield damage effect: 'unapply' effect is linked to getFluxDissipation(), rather than getShieldDamageTakenMult().
3. 'Technology' aptitude, 'Computer Systems' & 'Mechanical Engineering' skills, as well as the 'Minaturized Capacitors/Vents' (both) and 'Optimized Assembly' perks all have an incorrect ScopeDescription; currently they are set to 'ScopeDescription.ALL_SHIPS', whereas they should be 'ScopeDescription.FLEET'.
4. 'Command Experience' skill, 'Making Do' perk: the current 'getEffectDescription':
return "" + (int)(SkillData.COMMAND_EXPERIENCE_MIN_CREW_MULT * 100f) + "% less crew required to take ships into combat";
will not display a correct value if the end-user edits the:
public static final float COMMAND_EXPERIENCE_MIN_CREW_MULT = 0.5f;
in SkillData.java to a greater numerical value (say, 0.75f) and expects to see a 75% reduction in minimum crew requirements; currently, it will set it to that exact value (only a 25% reduction).
Changing the 'apply' effect to:
stats.getMinCrewMod().modifyMult(id, 1f - SkillData.COMMAND_EXPERIENCE_MIN_CREW_MULT);
seems to be the most straight-forward solution.