The average bittorrent-client has 'some' intelligence.
When you add a torrent to the client AND the content is NOT already at the location where the client expected it to be, the client 'knows' the content is NOT there.
When you later add the content, the client still remembered the content wasn't there and won't look for it again.
Thats why the forced hashcheck is required to let the client figure out the content is there, for what reason.
When the hash doesn't match it now knows for sure downloading is required

When the tracker 'shows as downloaded', the client has told the tracker there was some downloading done at some point.
YOU could/should have seen the client had started downloading something.
More exact YOU told the client to download. By setting (autostart torrents) or manually.
Bottomline: don't blame the tracker or your bittorrent-client. YOU are to blame!

Never let a client autostart torrents. It can screw things when YOU make a mistake.