The 1862 Shiloh scenario has an issue with regional decisions. Specifically, the script creating the scenario never changes the faction selection before running the command that creates the regional decisions. The end result is that the CSA gets regional decisions it should not have (like "Unionists") and the USA gets no regional decisions at all.
Below are the relevant lines from the Shiloh scenario script, "ScriptShiloh62.ini". As you can see, the last faction selection before ChgRgnDecisionFP is run is from the CSA_Blocked_Ports.inc file (CSA). After that, the ChgRgnDecisionFP command is run twice with no faction selection change. If all of those decisions had been meant for one faction, they probably would have been put in one command. I believe they were intended to be run with a faction selection change in between them.
SelectFaction = USA
SetFacRelationships = CSA;-100
NULL = NULL
CitiesShiloh62.inc
CSA_Blocked_Ports.inc
ChgRgnDecisionFP = $rgdPlunder;2;$rgdDefensiveWorks;1;$rgdScorchedEarth;1;$rgdLandMine;1;$rgdPartisansRaid;2;$rgdPartisansAmbush;2;$rgdUSPartisansCreate;2;$rgdUnionists;1;$rgdSeaMine;2
ChgRgnDecisionFP = $rgdPlunder;2;$rgdDefensiveWorks;1;$rgdScorchedEarth;2;$rgdLandMine;3;$rgdPartisansRaid;2;$rgdPartisansAmbush;2;$rgdCSPartisansCreate;2;$rgdCopperheads;1;$rgdSeaMine;1
NULL = NULL
NULL = NULL
NULL = NULL