At the moment building the Hyperion Logistics System does not raise your logistics cap (the maximum number of logistics points for a fleet).

To correct it, the following xml (found in the ImprovementDefs.xml file):

<Improvement>
<InternalName>HyperionLogisticsSystem</InternalName>
...
<LevelEffectStats>
<EffectType>LogisticsCap</EffectType>
<Scope>Global</Scope>
<Target>
<TargetType>Faction</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>0.05</Value>
</LevelEffectStats>
...
</Improvement>

should be changed to:

<Improvement>
<InternalName>HyperionLogisticsSystem</InternalName>
...
<LevelEffectStats>
<EffectType>LogisticsCap</EffectType>
<Scope></Scope>
<Target>
<TargetType>Faction</TargetType>
</Target>
<BonusType>Multiplier</BonusType>
<Value>0.05</Value>
</LevelEffectStats>
...
</Improvement>