diff --git a/src/DIRAC/DataManagementSystem/Utilities/ResolveSE.py b/src/DIRAC/DataManagementSystem/Utilities/ResolveSE.py
index dd5d3149459..0eccbec8fdb 100644
--- a/src/DIRAC/DataManagementSystem/Utilities/ResolveSE.py
+++ b/src/DIRAC/DataManagementSystem/Utilities/ResolveSE.py
@@ -1,6 +1,7 @@
 """ This module allows to resolve output SEs for Job based
 on SE and site/country association
 """
+
 from random import shuffle
 
 from DIRAC import gLogger, gConfig
@@ -70,7 +71,6 @@ def getDestinationSEList(outputSE, site, outputmode="Any"):
         raise RuntimeError(localSEs["Message"])
     localSEs = localSEs["Value"]
     sLog.verbose("Local SE list is:", ", ".join(localSEs))
-
     # There is an alias defined for this Site
     associatedSEs = gConfig.getValue(f"/Resources/Sites/{prefix}/{site}/AssociatedSEs/{outputSE}", [])
     if associatedSEs:
diff --git a/src/DIRAC/TransformationSystem/Agent/TransformationAgent.py b/src/DIRAC/TransformationSystem/Agent/TransformationAgent.py
index b1b5a45ad11..02da4ea5b5d 100644
--- a/src/DIRAC/TransformationSystem/Agent/TransformationAgent.py
+++ b/src/DIRAC/TransformationSystem/Agent/TransformationAgent.py
@@ -8,6 +8,7 @@
   :dedent: 2
   :caption: TransformationAgent options
 """
+
 import time
 import os
 import datetime
@@ -241,7 +242,7 @@ def processTransformation(self, transDict, clients):
         if transID not in self.replicaCache:
             self.__readCache(transID)
         transFiles = transFiles["Value"]
-        unusedLfns = [f["LFN"] for f in transFiles]
+        unusedLfns = {f["LFN"] for f in transFiles}
         unusedFiles = len(unusedLfns)
 
         plugin = transDict.get("Plugin", "Standard")
@@ -250,7 +251,7 @@ def processTransformation(self, transDict, clients):
             maxFiles = Operations().getValue(f"TransformationPlugins/{plugin}/MaxFilesToProcess", 0)
             # Get plugin-specific limit in number of files (0 means no limit)
             totLfns = len(unusedLfns)
-            lfnsToProcess = self.__applyReduction(unusedLfns, maxFiles=maxFiles)
+            lfnsToProcess = set(self.__applyReduction(unusedLfns, maxFiles=maxFiles))
             if len(lfnsToProcess) != totLfns:
                 self._logInfo(
                     "Reduced number of files from %d to %d" % (totLfns, len(lfnsToProcess)),
@@ -533,8 +534,10 @@ def _getDataReplicasDM(self, transID, lfns, clients, forJobs=True, ignoreMissing
             method=method,
             transID=transID,
         )
+        successful_set = set(replicas["Successful"])
+        failed_set = set(replicas["Failed"])
         # If files are neither Successful nor Failed, they are set problematic in the FC
-        problematicLfns = [lfn for lfn in lfns if lfn not in replicas["Successful"] and lfn not in replicas["Failed"]]
+        problematicLfns = [lfn for lfn in lfns if lfn not in successful_set and lfn not in failed_set]
         if problematicLfns:
             self._logInfo(f"{len(problematicLfns)} files found problematic in the catalog, set ProbInFC")
             res = clients["TransformationClient"].setFileStatusForTransformation(