Possible interference with Focal Point module

I had the same issue. I have solved this by checking the filefields_paths_entity_update hook and modifying it in my custom module like this:

use Drupal\media\MediaInterface;
use Drupal\Core\Entity\EntityInterface;
use Drupal\filefield_paths\Utility\FieldItem;

/**
 * Implements hook_entity_update().
 */
function pixelthis_entity_update(EntityInterface $entity) {

  if (!$entity instanceof MediaInterface || $entity->bundle() !== 'image') {
    return;
  }

  // The filefield_paths module conflicts with the focal_point module.
  // If the filefield_paths module is enabled, we need to disable it
  // for the media.image.field_media_image field.
  // other wise the focal point will not work.
  // https://www.drupal.org/project/filefield_paths/issues/3015137
  $module_handler = \Drupal::moduleHandler();
  foreach ($entity->getFields() as $field) {
    if (FieldItem::hasConfigurationEnabled($field)) {
      $settings = FieldItem::getConfiguration($field);
      // Invoke hook_filefield_paths_process_file().
      $module_handler->invokeAll(
        'filefield_paths_process_file',
        [$entity, $field, $settings]
      );
    }
  }

}

Applying the patch in #3042259: Focal point location is not saved if others module change URI on first save. resolved this for us.

This one is on us, so it is fixed here rather than in Focal Point.

When a file is moved into its token based path, the field item still points at the pre-move file. Focal Point reads the field item immediately after us and saves its crop against a location that no longer exists, which is why the position is lost on the first save and correct on the second. Any module that reads a file path after us hits the same thing.

MR !75 points the field item at the moved file, with kernel tests covering it. There is no dependency on Focal Point or Crop.

Worth noting that https://www.drupal.org/i/3042259 is still Needs Review, so the patch people have been applying has not shipped. The two fixes are complementary and both are worth having.

Credit to Nuuou for the report and reproduction, tvhung for finding the cause in 2019, nikitas for the workaround, and justcaldwell for confirming it and opening the Focal Point MR.