diff --git a/beacon-chain/state/state-native/setters_misc.go b/beacon-chain/state/state-native/setters_misc.go
index bf855bcd6..e5c4b4e65 100644
--- a/beacon-chain/state/state-native/setters_misc.go
+++ b/beacon-chain/state/state-native/setters_misc.go
@@ -6,6 +6,7 @@ import (
 	"github.com/prysmaticlabs/prysm/v5/beacon-chain/state/stateutil"
 	fieldparams "github.com/prysmaticlabs/prysm/v5/config/fieldparams"
 	"github.com/prysmaticlabs/prysm/v5/consensus-types/primitives"
+	"github.com/prysmaticlabs/prysm/v5/container/slice"
 	"github.com/prysmaticlabs/prysm/v5/crypto/hash"
 	"github.com/prysmaticlabs/prysm/v5/encoding/bytesutil"
 	ethpb "github.com/prysmaticlabs/prysm/v5/proto/prysm/v1alpha1"
@@ -198,9 +199,14 @@ func (b *BeaconState) addDirtyIndices(index types.FieldIndex, indices []uint64)
 		return
 	}
 	totalIndicesLen := len(b.dirtyIndices[index]) + len(indices)
+	// Reduce duplicates to verify that these are indeed unique.
+	if totalIndicesLen > indicesLimit {
+		b.dirtyIndices[index] = slice.SetUint64(b.dirtyIndices[index])
+		totalIndicesLen = len(b.dirtyIndices[index]) + len(indices)
+	}
 	if totalIndicesLen > indicesLimit {
 		b.rebuildTrie[index] = true
-		b.dirtyIndices[index] = []uint64{}
+		b.dirtyIndices[index] = make([]uint64, 0, indicesLimit)
 	} else {
 		b.dirtyIndices[index] = append(b.dirtyIndices[index], indices...)
 	}
diff --git a/beacon-chain/state/state-native/state_test.go b/beacon-chain/state/state-native/state_test.go
index a7070d886..faed7b7f6 100644
--- a/beacon-chain/state/state-native/state_test.go
+++ b/beacon-chain/state/state-native/state_test.go
@@ -416,6 +416,26 @@ func TestCopyAllTries(t *testing.T) {
 	assert.NotEqual(t, rt, newRt)
 }
 
+func TestDuplicateDirtyIndices(t *testing.T) {
+	newState := &BeaconState{
+		rebuildTrie:  make(map[types.FieldIndex]bool),
+		dirtyIndices: make(map[types.FieldIndex][]uint64),
+	}
+	for i := uint64(0); i < indicesLimit-5; i++ {
+		newState.dirtyIndices[types.Balances] = append(newState.dirtyIndices[types.Balances], i)
+	}
+	// Append duplicates
+	newState.dirtyIndices[types.Balances] = append(newState.dirtyIndices[types.Balances], []uint64{0, 1, 2, 3, 4}...)
+
+	// We would remove the duplicates and stay under the threshold
+	newState.addDirtyIndices(types.Balances, []uint64{9997, 9998})
+	assert.Equal(t, false, newState.rebuildTrie[types.Balances])
+
+	// We would trigger above the threshold.
+	newState.addDirtyIndices(types.Balances, []uint64{10000, 10001, 10002, 10003})
+	assert.Equal(t, true, newState.rebuildTrie[types.Balances])
+}
+
 func generateState(t *testing.T) state.BeaconState {
 	count := uint64(100)
 	vals := make([]*ethpb.Validator, 0, count)
diff --git a/container/slice/slice.go b/container/slice/slice.go
index 2cd81f96d..c39c371d3 100644
--- a/container/slice/slice.go
+++ b/container/slice/slice.go
@@ -94,7 +94,7 @@ func UnionUint64(s ...[]uint64) []uint64 {
 // values from the provided list of indices.
 func SetUint64(a []uint64) []uint64 {
 	// Remove duplicates indices.
-	intMap := map[uint64]bool{}
+	intMap := make(map[uint64]bool, len(a))
 	cleanedIndices := make([]uint64, 0, len(a))
 	for _, idx := range a {
 		if intMap[idx] {