Yeah, that can happen. You have to train the filter & it takes a while
That's why I think it's a good idea to display junk...just in case some good files slip through the net.
If you think files have been wrongly labelled as junk, you can always download some of the file, preview it & see what it's like. If it turns out to be a good file, label it as 'not junk'. Don't forget to look up the file with Bitzi before download. Music files aren't rated very often & I'm not sure about program files (might be?) but a lot of video gets rated.
How to use Bitzi

You can change how strictly you've set the junk filter too. Have a look through the thread below. It's a bit long but has some good info & tips
Junk Filter