diff --git a/acceptance/bundle/templates/dbt-sql/output.txt b/acceptance/bundle/templates/dbt-sql/output.txt
index 972c7e1529..efd8be8157 100644
--- a/acceptance/bundle/templates/dbt-sql/output.txt
+++ b/acceptance/bundle/templates/dbt-sql/output.txt
@@ -22,6 +22,7 @@ Workspace:
 Validation OK!
 
 >>> $CLI bundle validate -t prod
+11:31:28  WARN target with 'mode: production' should specify an explicit 'targets.prod.git' configuration pid=20104 mutator=initialize mutator=seq mutator=ProcessTargetMode
 Name: my_dbt_sql
 Target: prod
 Workspace:
diff --git a/acceptance/bundle/templates/default-python/output.txt b/acceptance/bundle/templates/default-python/output.txt
index 5493ac2cf7..6db329b5b9 100644
--- a/acceptance/bundle/templates/default-python/output.txt
+++ b/acceptance/bundle/templates/default-python/output.txt
@@ -20,6 +20,7 @@ Workspace:
 Validation OK!
 
 >>> $CLI bundle validate -t prod
+11:31:29  WARN target with 'mode: production' should specify an explicit 'targets.prod.git' configuration pid=20387 mutator=initialize mutator=seq mutator=ProcessTargetMode
 Name: my_default_python
 Target: prod
 Workspace:
diff --git a/acceptance/bundle/templates/default-sql/output.txt b/acceptance/bundle/templates/default-sql/output.txt
index fe01390931..b4fd270af8 100644
--- a/acceptance/bundle/templates/default-sql/output.txt
+++ b/acceptance/bundle/templates/default-sql/output.txt
@@ -22,6 +22,7 @@ Workspace:
 Validation OK!
 
 >>> $CLI bundle validate -t prod
+11:31:29  WARN target with 'mode: production' should specify an explicit 'targets.prod.git' configuration pid=20374 mutator=initialize mutator=seq mutator=ProcessTargetMode
 Name: my_default_sql
 Target: prod
 Workspace:
diff --git a/bundle/mutator.go b/bundle/mutator.go
index 6c9968aacd..462d53d3f9 100644
--- a/bundle/mutator.go
+++ b/bundle/mutator.go
@@ -35,17 +35,7 @@ func Apply(ctx context.Context, b *Bundle, m Mutator) diag.Diagnostics {
 		}
 	}()
 
-	diags := m.Apply(ctx, b)
-
-	// Log error in diagnostics if any.
-	// Note: errors should be logged when constructing them
-	// such that they are not logged multiple times.
-	// If this is done, we can omit this block.
-	if err := diags.Error(); err != nil {
-		log.Errorf(ctx, "Error: %s", err)
-	}
-
-	return diags
+	return m.Apply(ctx, b)
 }
 
 type funcMutator struct {
diff --git a/bundle/mutator_read_only.go b/bundle/mutator_read_only.go
index ee4e36e0fa..777198f13e 100644
--- a/bundle/mutator_read_only.go
+++ b/bundle/mutator_read_only.go
@@ -20,10 +20,5 @@ func ApplyReadOnly(ctx context.Context, rb ReadOnlyBundle, m ReadOnlyMutator) di
 	ctx = log.NewContext(ctx, log.GetLogger(ctx).With("mutator (read-only)", m.Name()))
 
 	log.Debugf(ctx, "ApplyReadOnly")
-	diags := m.Apply(ctx, rb)
-	if err := diags.Error(); err != nil {
-		log.Errorf(ctx, "Error: %s", err)
-	}
-
-	return diags
+	return m.Apply(ctx, rb)
 }
diff --git a/cmd/root/root.go b/cmd/root/root.go
index 3b37d01769..4d0d425624 100644
--- a/cmd/root/root.go
+++ b/cmd/root/root.go
@@ -114,10 +114,15 @@ func Execute(ctx context.Context, cmd *cobra.Command) error {
 		if err == nil {
 			logger.Info("completed execution",
 				slog.String("exit_code", "0"))
+		} else if errors.Is(err, ErrAlreadyPrinted) {
+			logger.Debug("failed execution",
+				slog.String("exit_code", "1"),
+			)
 		} else {
 			logger.Error("failed execution",
 				slog.String("exit_code", "1"),
-				slog.String("error", err.Error()))
+				slog.String("error", err.Error()),
+			)
 		}
 	}
 
diff --git a/libs/flags/log_level_flag.go b/libs/flags/log_level_flag.go
index 836d84b700..82e2abc4c3 100644
--- a/libs/flags/log_level_flag.go
+++ b/libs/flags/log_level_flag.go
@@ -25,7 +25,7 @@ type LogLevelFlag struct {
 
 func NewLogLevelFlag() LogLevelFlag {
 	return LogLevelFlag{
-		l: log.LevelDisabled,
+		l: log.LevelWarn,
 	}
 }