-                    for f in info_dict['requested_formats']:
-                        new_info = dict(info_dict)
-                        new_info.update(f)
-                        fname = self.prepare_filename(new_info)
-                        fname = prepend_extension(fname, 'f%s' % f['format_id'])
-                        downloaded.append(fname)
-                        partial_success = dl(fname, new_info)
-                        success = success and partial_success
-                    info_dict['__postprocessors'] = postprocessors
-                    info_dict['__files_to_merge'] = downloaded
+
+                    def compatible_formats(formats):
+                        video, audio = formats
+                        # Check extension
+                        video_ext, audio_ext = audio.get('ext'), video.get('ext')
+                        if video_ext and audio_ext:
+                            COMPATIBLE_EXTS = (
+                                ('mp3', 'mp4', 'm4a', 'm4p', 'm4b', 'm4r', 'm4v'),
+                                ('webm')
+                            )
+                            for exts in COMPATIBLE_EXTS:
+                                if video_ext in exts and audio_ext in exts:
+                                    return True
+                        # TODO: Check acodec/vcodec
+                        return False
+
+                    filename_real_ext = os.path.splitext(filename)[1][1:]
+                    filename_wo_ext = (
+                        os.path.splitext(filename)[0]
+                        if filename_real_ext == info_dict['ext']
+                        else filename)
+                    requested_formats = info_dict['requested_formats']
+                    if self.params.get('merge_output_format') is None and not compatible_formats(requested_formats):
+                        info_dict['ext'] = 'mkv'
+                        self.report_warning('You have requested formats incompatible for merge. '
+                                            'The formats will be merged into mkv')
+                    # Ensure filename always has a correct extension for successful merge
+                    filename = '%s.%s' % (filename_wo_ext, info_dict['ext'])
+                    if os.path.exists(encodeFilename(filename)):
+                        self.to_screen(
+                            '[download] %s has already been downloaded and '
+                            'merged' % filename)
+                    else:
+                        for f in requested_formats:
+                            new_info = dict(info_dict)
+                            new_info.update(f)
+                            fname = self.prepare_filename(new_info)
+                            fname = prepend_extension(fname, 'f%s' % f['format_id'], new_info['ext'])
+                            downloaded.append(fname)
+                            partial_success = dl(fname, new_info)
+                            success = success and partial_success
+                        info_dict['__postprocessors'] = postprocessors
+                        info_dict['__files_to_merge'] = downloaded