I can't reproduce the error:
File: /path/to/file/test.sql
SELECT VERSION();
SELECT 'system' `system`;
system ls -al myDir
SELECT '\\!';
\! ls -al myDir
MySQL Command Line:
mysql> \. /path/to/file/test.sql
+-----------+
| VERSION() |
+-----------+
| 5.7.11 |
+-----------+
1 row in set (0.00 sec)
+--------+
| system |
+--------+
| system |
+--------+
1 row in set (0.00 sec)
total 0
dr-------- 2 user user 10 Jan 12 00:00 .
dr-------- 23 user user 280 Jan 13 23:00 ..
+----+
| \! |
+----+
| \! |
+----+
1 row in set (0.00 sec)
total 0
dr-------- 2 user user 10 Jan 12 00:00 .
dr-------- 23 user user 280 Jan 13 23:00 ..
The system (\!) command works only in Unix., see 4.5.1.2 mysql Commands. Try using Windows Subsystem for Linux (WSL), see Windows 10 Installation Guide.