Repairing Clean URL and Fixing Errors from System Log

Hi All,
I have a multilingual website built with Drupal 8.3.1 and the default language is Vietnamese while English is the second one. Serving from my default language is fine, all urls are clean. But when switching to English, urls of pages on this English site has “index.php/” with it, for instance, mydomain.org/index.php/en/news etc. One more strange thing is this applies for only anonymous browsings. If I login to the site, both Vietnamese and English sites work as expected. I have tried to use different language detection methods such as url path prefix, selected language and user preferences but cannot solve. And also read from other discussions to change the RewriteRule in .htaccess but it doesn’t solve as well.
Besides, I also have error log messages such as linkit_filter, page not found etc and I would like to have someone with Drupal experiences to solve all of these problems. Anyone is interested in this work, please contact me. Thanks.

Drupal version: 


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