The method \Drupal\file\FileRepository::loadByUri use the \Drupal\Core\Entity\EntityHandlerBase::loadByProperties to load the files by uri property. When multiple files match to the uri the code loop throught the $files to break the loop and returns the first match, the problem is with the usage of the method loadByProperties, the results are sorted by chronological order.
Run the code $files = \Drupal::entityTypeManager()->getStorage('file')->loadByProperties(); and checks the array keys (which are files IDs), they are in chronological order.
Use the entity query instead the loadByProperty method as following code :
$fids = $fileStorage
->getQuery()
->condition('uri', $uri)
->accessCheck(FALSE)
->sort('fid', 'DESC')
->execute();
/** @var \Drupal\file\FileInterface[] $files */
$files = $fileStorage->loadMultiple($fids);
Needs work
10.1 ✨
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