diff --git a/internal/script/script.go b/internal/script/script.go
index 1fe759ad..171741fb 100644
--- a/internal/script/script.go
+++ b/internal/script/script.go
@@ -259,6 +259,7 @@ declare -A pids=()
 declare -A exitcodes=()
 declare -A orig_names=()
 current_seq_pid=""
+current_seq_script=""
 
 continue_on_script_error={{if .ContinueOnScriptError}}1{{else}}0{{end}}
 
@@ -290,6 +291,7 @@ start_concurrent_scripts() {
 run_sequential_scripts() {
   for s in "${sequential_scripts[@]}"; do
     current_seq_pid=""
+    current_seq_script="$s"
     setsid bash "$script_dir/${s}.sh" > "$script_dir/${s}.stdout" 2> "$script_dir/${s}.stderr" &
     current_seq_pid=$!
     pids[$s]=$current_seq_pid
@@ -304,6 +306,7 @@ run_sequential_scripts() {
       fi
     fi
     current_seq_pid=""
+    current_seq_script=""
   done
 }
 
@@ -314,10 +317,17 @@ kill_script() {
   if ! ps -p "$pid" > /dev/null 2>&1; then return 0; fi
   # Send signal to the process group (negative PID)
   kill -SIGINT -"$pid" 2>/dev/null || true
-  # Give it a moment to clean up
-  sleep 0.1
+  # Give it time to clean up so child script can finalize
+  # Wait up to 5 seconds in 0.5s intervals
+  local waited=0
+  while ps -p "$pid" > /dev/null 2>&1 && [ "$waited" -lt 10 ]; do
+    sleep 0.5
+    waited=$((waited + 1))
+  done
   # Force kill the process group if still alive
-  kill -SIGKILL -"$pid" 2>/dev/null || true
+  if ps -p "$pid" > /dev/null 2>&1; then
+    kill -SIGKILL -"$pid" 2>/dev/null || true
+  fi
   wait "$pid" 2>/dev/null || true
   if [[ -z "${exitcodes[$s]:-}" ]]; then exitcodes[$s]=130; fi
 }
@@ -351,11 +361,8 @@ handle_sigint() {
     kill_script "$s"
   done
   # kill current sequential script if running
-  if [[ -n "$current_seq_pid" ]]; then
-    kill -SIGINT -"$current_seq_pid" 2>/dev/null || true
-    sleep 0.1
-    kill -SIGKILL -"$current_seq_pid" 2>/dev/null || true
-    wait "$current_seq_pid" 2>/dev/null || true
+  if [[ -n "$current_seq_script" ]]; then
+    kill_script "$current_seq_script"
   fi
   print_summary
   rm -f {{.ControllerPIDFile}}
diff --git a/internal/script/scripts.go b/internal/script/scripts.go
index 2848c53d..ab42faa9 100644
--- a/internal/script/scripts.go
+++ b/internal/script/scripts.go
@@ -1462,11 +1462,11 @@ fi
 stop_profiling() {
     if [ -n "$perf_fp_pid" ]; then
         kill -0 "$perf_fp_pid" 2>/dev/null && kill -INT "$perf_fp_pid"
-        wait "$perf_fp_pid"
+        wait "$perf_fp_pid" || true
     fi
     if [ -n "$perf_dwarf_pid" ]; then
         kill -0 "$perf_dwarf_pid" 2>/dev/null && kill -INT "$perf_dwarf_pid"
-        wait "$perf_dwarf_pid"
+        wait "$perf_dwarf_pid" || true
     fi
     for pid in "${java_pids[@]}"; do
         async-profiler/bin/asprof stop -o collapsed -f ap_folded_"$pid" "$pid"
@@ -1518,8 +1518,14 @@ print_results() {
     done
 }
 
+_finalize=0 # flag to indicate if finalize has been called
+
 # Function to finalize profiling and output
 finalize() {
+    if [ $_finalize -eq 1 ]; then
+        return
+    fi
+    _finalize=1
     stop_profiling
     collapse_perf_data
     print_results
@@ -1584,16 +1590,18 @@ for pid in "${java_pids[@]}"; do
 done
 
 # profiling has been started, set up trap to finalize on interrupt
-trap finalize INT TERM
+trap finalize INT TERM EXIT
 
-# Wait for the specified duration (seconds), then wrap it up by calling finalize
+# wait
 if [ "$duration" -gt 0 ]; then
+    # wait for the specified duration (seconds), then wrap it up by calling finalize
     sleep "$duration"
-    finalize
+else
+    # wait indefinitely until child processes are killed or interrupted
+    wait
 fi
 
-# Wait indefinitely until interrupted, trap will call finalize
-wait
+finalize
 `,
 		Superuser:  true,
 		Sequential: true,
diff --git a/internal/workflow/signals.go b/internal/workflow/signals.go
index 58fb935e..4e34aff2 100644
--- a/internal/workflow/signals.go
+++ b/internal/workflow/signals.go
@@ -5,6 +5,7 @@ package workflow
 
 import (
 	"context"
+	"fmt"
 	"log/slog"
 	"os"
 	"os/exec"
@@ -31,7 +32,10 @@ func signalProcessOnTarget(t target.Target, pidStr string, sigStr string) error
 	} else {
 		cmd = exec.Command("kill", sigStr, pidStr)
 	}
-	_, _, _, err := t.RunCommandEx(cmd, 5, false, true) // #nosec G204
+	// waitTime must exceed the controller script's kill_script graceful shutdown period (5s)
+	// plus buffer for network latency when working with remote targets
+	waitTime := 15
+	_, _, _, err := t.RunCommandEx(cmd, waitTime, false, true) // #nosec G204
 	return err
 }
 
@@ -55,9 +59,6 @@ func configureSignalHandler(myTargets []target.Target, statusFunc progress.Multi
 	go func() {
 		sig := <-sigChannel
 		slog.Debug("received signal", slog.String("signal", sig.String()))
-		// The controller.sh script is run in its own process group, so we need to send the signal
-		// directly to the PID of the controller. For every target, look for the primary_collection_script
-		// PID file and send SIGINT to it.
 		// The controller script is run in its own process group, so we need to send the signal
 		// directly to the PID of the controller. For every target, look for the controller
 		// PID file and send SIGINT to it.
@@ -69,6 +70,7 @@ func configureSignalHandler(myTargets []target.Target, statusFunc progress.Multi
 			stdout, _, exitcode, err := t.RunCommandEx(exec.Command("cat", pidFilePath), 5, false, true) // #nosec G204
 			if err != nil {
 				slog.Error("error retrieving target controller PID", slog.String("target", t.GetName()), slog.String("error", err.Error()))
+				continue
 			}
 			if exitcode == 0 {
 				pidStr := strings.TrimSpace(stdout)
@@ -86,18 +88,20 @@ func configureSignalHandler(myTargets []target.Target, statusFunc progress.Multi
 			ctx, cancel := context.WithTimeout(context.Background(), targetTimeout)
 			timedOut := false
 			pidFilePath := filepath.Join(t.GetTempDirectory(), script.ControllerPIDFileName)
+			// read the pid file
+			stdout, _, exitcode, err := t.RunCommandEx(exec.Command("cat", pidFilePath), 5, false, true) // #nosec G204
+			if err != nil || exitcode != 0 {
+				slog.Debug("target controller PID file no longer exists, assuming script has exited or is in the process of exiting", slog.String("target", t.GetName()))
+				cancel()
+				continue
+			}
+			pidStr := strings.TrimSpace(stdout)
 			for {
-				// read the pid file
-				stdout, _, exitcode, err := t.RunCommandEx(exec.Command("cat", pidFilePath), 5, false, true) // #nosec G204
-				if err != nil || exitcode != 0 {
-					// pid file doesn't exist
-					break
-				}
-				pidStr := strings.TrimSpace(stdout)
 				// determine if the process still exists
 				_, _, exitcode, err = t.RunCommandEx(exec.Command("ps", "-p", pidStr), 5, false, true) // #nosec G204
 				if err != nil || exitcode != 0 {
-					break // process no longer exists, script has exited
+					slog.Debug("target controller process no longer exists", slog.String("target", t.GetName()))
+					break
 				}
 				// check for timeout
 				select {
@@ -122,8 +126,26 @@ func configureSignalHandler(myTargets []target.Target, statusFunc progress.Multi
 			cancel()
 		}
 
-		// send SIGINT to perfspect's children
-		err := util.SignalChildren(syscall.SIGINT)
+		// Race condition between the controller script deleting its PID file and it truly exiting.
+		// Future work: reconsider decision to have the controller script delete its own PID file.
+		// When working with a remote target we want to give our local SSH command time to exit cleanly
+		// before we send SIGINT to it. If we interrupt the SSH command unnecessarily, the controller output
+		// will be lost.
+		time.Sleep(500 * time.Millisecond)
+
+		// send SIGINT to perfspect's remaining children, if any
+		myPid := os.Getpid()
+		children, err := util.GetChildren(myPid)
+		if err != nil {
+			slog.Error("error retrieving child processes", slog.String("error", err.Error()))
+			return
+		}
+		if len(children) == 0 {
+			slog.Debug("no child processes to signal")
+			return
+		}
+		slog.Debug("signaling child processes", slog.String("child PIDs", fmt.Sprintf("%v", children)))
+		err = util.SignalChildren(syscall.SIGINT)
 		if err != nil {
 			slog.Error("error sending signal to children", slog.String("error", err.Error()))
 		}