diff --git a/src/db/db/dbAsIfFlatRegion.cc b/src/db/db/dbAsIfFlatRegion.cc
index 37b1708ee..7ba74217e 100644
--- a/src/db/db/dbAsIfFlatRegion.cc
+++ b/src/db/db/dbAsIfFlatRegion.cc
@@ -1237,7 +1237,12 @@ AsIfFlatRegion::run_check (db::edge_relation_type rel, bool different_polygons,
     different_polygons = true;
   }
 
-  bool needs_merged_primary = (! other && different_polygons) || options.needs_merged ();
+  //  in some cases we need merged primary polygons:
+  //  1.) isolated check (same layer, but different polygons)
+  //  2.) options need merged edges (projection limits, rectangle filter, opposite filter)
+  //  3.) prop_ne constraint - in that case, merge must not be applied internally after properties have been separated
+  bool needs_merged_primary = (! other && different_polygons) || options.needs_merged () || pc_always_different (options.prop_constraint);
+
   bool primary_is_merged = is_merged ();
   db::RegionIterator polygons;
 
diff --git a/src/db/db/dbDeepRegion.cc b/src/db/db/dbDeepRegion.cc
index bb739ed54..ea984a1a8 100644
--- a/src/db/db/dbDeepRegion.cc
+++ b/src/db/db/dbDeepRegion.cc
@@ -2405,7 +2405,12 @@ DeepRegion::run_check (db::edge_relation_type rel, bool different_polygons, cons
 
   //  primary input
 
-  bool needs_merged_primary = (! other_deep && different_polygons) || options.needs_merged ();
+  //  in some cases we need merged primary polygons:
+  //  1.) isolated check (same layer, but different polygons)
+  //  2.) options need merged edges (projection limits, rectangle filter, opposite filter)
+  //  3.) prop_ne constraint - in that case, merge must not be applied internally after properties have been separated
+  bool needs_merged_primary = (! other_deep && different_polygons) || options.needs_merged () || pc_always_different (options.prop_constraint);
+
   bool primary_is_merged = false;
 
   db::DeepLayer polygons;
diff --git a/src/drc/unit_tests/drcSimpleTests.cc b/src/drc/unit_tests/drcSimpleTests.cc
index 9928e45de..a4a2b489f 100644
--- a/src/drc/unit_tests/drcSimpleTests.cc
+++ b/src/drc/unit_tests/drcSimpleTests.cc
@@ -2143,3 +2143,14 @@ TEST(151d_edges_from_region_with_properties)
 {
   run_test (_this, "151", true);
 }
+
+// issue #2416
+TEST(152_sep_with_props)
+{
+  run_test (_this, "152", false);
+}
+
+TEST(152d_sep_with_props)
+{
+  run_test (_this, "152", true);
+}
diff --git a/testdata/drc/drcSimpleTests_152.drc b/testdata/drc/drcSimpleTests_152.drc
new file mode 100644
index 000000000..17f0b6af2
--- /dev/null
+++ b/testdata/drc/drcSimpleTests_152.drc
@@ -0,0 +1,25 @@
+source $drc_test_source
+target $drc_test_target
+
+if $drc_test_deep
+  deep
+end
+
+deep
+
+l1 = input(1, 0, enable_props)
+l1.output(1, 0)
+
+l2 = input(2, 0, enable_props)
+l2.output(2, 0)
+
+l1.sep(l2, 1.um, props_ne).output(100, 0)
+l1.sep(l2, 1.um, props_eq).output(101, 0)
+l1.sep(l2, 1.um).output(102, 0)
+l2.sep(l1, 1.um, props_ne).output(110, 0)
+l2.sep(l1, 1.um, props_eq).output(111, 0)
+l2.sep(l1, 1.um).output(112, 0)
+l1.space(1.um, props_ne).output(120, 0)
+l1.space(1.um, props_eq).output(121, 0)
+l1.space(1.um).output(122, 0)
+
diff --git a/testdata/drc/drcSimpleTests_152.gds b/testdata/drc/drcSimpleTests_152.gds
new file mode 100644
index 000000000..9835938cd
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diff --git a/testdata/drc/drcSimpleTests_au152.gds b/testdata/drc/drcSimpleTests_au152.gds
new file mode 100644
index 000000000..523f55b6b
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diff --git a/testdata/drc/drcSimpleTests_au152d.gds b/testdata/drc/drcSimpleTests_au152d.gds
new file mode 100644
index 000000000..71b367404
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