Upon completion, the download is placed in download file instead of torrents file... even though in settings the completed file is the torrents file.  Why is that?

Settings /transfers/local files the first choice sets where you start the torrent. The second choice, if checked moves the file to this location upon completion. I suspect you will find the answer to your question by looking there.

Apologies if this is not quite the same problem.

Situation: Linux

Folder structure:
~/Torrents
~/Torrents/Incomplete
~/Torrents/Torrent files

Tixati Settings:

Default download location - ~/Torrents/Incomplete
Upon completion, move to this location - ~/Torrents
Incomplete piece storage location - ~/Torrents/Incomplete

I don't really understand the difference between Default download location and Incomplete piece storage location? Also, why is the option to save the .torrent file not included. Personally, I don't want to download these and then open them, but when opening a torrent file in Tixati, the files are placed in ./tmp, so if I wanted to keep a file I'd need to move it manually...

Transfers/Meta-info: you can save .torrent file to your designated location.

From Tixati help page:

To save torrent files automatically go to Settings > Transfers > Meta-Info and select a folder under "Save a .torrent file in this folder when a new transfer starts". After that a copy of a torrent file for each started transfer will be saved in that location.

Thank you both. I missed the meta-info.