Do you have any message filters set up?

You can see the Junk log for its actions applied in Options > Security panel > Junk tab > Show log. If you have set up any message filters, use Tools > Message Filters > Filter log to see its log.

It should be clear if the Junk filter really moved the message and where to by looking at the first, or if any message filter was responsible by looking at the second.

hanks, Tonnes. I have no message filters set up. When I go to junk tab > Show log, the "show log" is not active. So still a mystery why some junk goes to Deleted folder. Any further advice?

Is it possible that your email provider is operating an anti-spam system and is moving messages automatically to Trash on your behalf?

Do you have more than one email account? Each has its own Junk Settings where you can set the destination for Junk messages. Maybe one account is set differently to the others?

Another option would be that if you use additonal software such as SpamPal, SpamAssasin etc. and enabled the Trust junk mail headers set by: setting in your Account Settings > Junk Settings section, that will cause email to be treated as Junk based on certain email headers that were added by the software, and those messages may not show up in the (internal) Junk Log, though I might be wrong here. You should be able to check the email sources (by pressing Ctrl-U or choosing the View > View Source item) for messages affected and find such additonal headers, for example X-SpamPal.

More info

Thanks all for your responses. I think I have found the answer. I had my junk setting to delete after 7 days! So I think the junk mail appearing in my delete folder were those ones, when I was later than usual deleting my junk files on a regular basis. I have set it now to 14 days and will keep an eye on it.