In AnomolyDefs.XML in the ...\My Games\GC3\Mods\Star Trek - Map Changers\Game\ folder remove the comment code  <!--   before each </Encounter> section like this
Glad you reminded me of this - Beginner is definitely too easy now - fixing the anomalies to be defended will make it a challenge.  Iin my first pass last night one of the initial Defenders was out scouting and ran into two Marque Ships from a Pirate Base - did not go well - got to watch out for Pirate bases now although it looks like the code is not creating ships initially or often at the Pirate Bases.
 
Anomaly Encounter Code Example:
  <Anomaly>
   <InternalName>LostScoutAnomoly</InternalName>
   <DisplayName>LostScoutAnomoly_Name</DisplayName>
   <Description>LostScoutAnomoly_Dec</Description>
   <ArtDefine>GraveyardAnomalyArt</ArtDefine>
   <Weight>15</Weight>
   <!--<EncounterChance>0.75</EncounterChance>
  <EncounterTriggers>
  <OnEvent>OnCollideAtAnomaly</OnEvent>
  <Target>
   <TargetType>Fleet</TargetType>
  </Target>
  <Lifetime>Instant</Lifetime>
  <PerformAction>
   <Action>BattleEncounter</Action>
   <StringParam>PirateEncounter</StringParam>
  </PerformAction>
  </EncounterTriggers>-->
 
Change the 7th line to become (i.e. remove each occurance of  <!--) :
<EncounterChance>0.75</EncounterChance>
Forgot about this from last time I did this have to also remove --> from the closing section of the EncounterTriggers Code too so line 18 of the code needs to change to:
 </EncounterTriggers>