The most likely cause is that those files were renamed manually at some point. When a filename has been manually modified, Zotero treats it as intentional and skips automatic renaming for that attachment going forward.

To reset them, you have two options:

• Rename Files... (what you've been using) -- resets all attachment filenames back to the template.
• The rename icon next to the filename in the attachment pane -- does the same for a single file if you only want to fix one at a time.

I did mean the name of the PDF file itself, in my File Explorer, i.e. filename.

It says "Zotero automatically renames files on disk based on parent item metadata such as the title and authors", and I set mine to be e.g. "Smith [2001] - The best study". However, Zotero for some reason, sometimes, just stops renaming them automatically.

I would link a PDF file to Zotero, then use Tools>Manage Attatchments>Convert Linked Files to Stored plus Normalize Attachment Titles. And for the most time it works as intended. But sometimes it would convert the file and write 'PDF' under parent item in Zotero, however, when I go "Left Click>Show File", the filename would still be "abcdf1221ff".

It would remain like that until I manually run Configure File Renaming>Rename Files. And yes, the options "Automatically rename files" as well as "Rename linked files" are ticked.

I think @tnajdek could be right, but I didn't have the time to test it with new and previously renamed files. I'm unsure if he meant that filename was renamed before putting it in Zotero or after, because I do not do that.