I generally read mail on my iPad. However, these days, Mail is so aggressive its removing some emails before I can even look at them. However, when I go to Junk, they're not there. Where is it puttering them?
Who is your ISP? It sounds like your ISP is filtering out spam mail before it gets to you. And that has nothing to do with the Mail app.... Log on to your ISP web page and see if there is a "spam" folder. I don't know who your ISP is but I use Gmail which does exactly that. I usually go thru the spam folder to make sure all the mail there is in fact spam or junk.