@@ -122,23 +122,28 @@ function updateParsedCommandLine(parsedCommandLine: ts.ParsedCommandLine, args:
 
         if (option) {
             // Ignore errors caused by tstl specific compiler options
-            const tsInvalidCompilerOptionErrorCode = 5023;
             parsedCommandLine.errors = parsedCommandLine.errors.filter(
-                e => !(e.code === tsInvalidCompilerOptionErrorCode && String(e.messageText).endsWith(`'${args[i]}'.`))
+                // TS5023: Unknown compiler option '{0}'.
+                // TS5025: Unknown compiler option '{0}'. Did you mean '{1}'?
+                e => !((e.code === 5023 || e.code === 5025) && String(e.messageText).includes(`'${args[i]}'.`))
             );
 
-            const { error, value, increment } = readCommandLineArgument(option, args[i + 1]);
+            const { error, value, consumed } = readCommandLineArgument(option, args[i + 1]);
             if (error) parsedCommandLine.errors.push(error);
             parsedCommandLine.options[option.name] = value;
-            i += increment;
+            if (consumed) {
+                i += 1;
+                // Values of custom options are parsed as a file name, exclude them
+                parsedCommandLine.fileNames = parsedCommandLine.fileNames.filter(f => f !== value);
+            }
         }
     }
 
     return parsedCommandLine;
 }
 
 interface CommandLineArgument extends ReadValueResult {
-    increment: number;
+    consumed: boolean;
 }
 
 function readCommandLineArgument(option: CommandLineOption, value: any): CommandLineArgument {
@@ -147,19 +152,19 @@ function readCommandLineArgument(option: CommandLineOption, value: any): Command
             value = value === "true";
         } else {
             // Set boolean arguments without supplied value to true
-            return { value: true, increment: 0 };
+            return { value: true, consumed: false };
         }
     }
 
     if (value === undefined) {
         return {
             error: cliDiagnostics.compilerOptionExpectsAnArgument(option.name),
             value: undefined,
-            increment: 0,
+            consumed: false,
         };
     }
 
-    return { ...readValue(option, value), increment: 1 };
+    return { ...readValue(option, value), consumed: true };
 }
 
 interface ReadValueResult {
 
@@ -9,10 +9,11 @@ describe("command line", () => {
     });
 
     test("should support standard typescript options", () => {
-        const commandLine = "--project tsconfig.json --noHeader -t es3 -lt 5.3";
+        const commandLine = "main.ts --project tsconfig.json --noHeader -t es3 -lt 5.3";
         const result = tstl.parseCommandLine(commandLine.split(" "));
 
         expect(result.errors).not.toHaveDiagnostics();
+        expect(result.fileNames).toEqual(["main.ts"]);
         expect(result.options).toEqual({
             project: "tsconfig.json",
             noHeader: true,