Problem started when I moved from the iphone 5 to iphone 6. The setup option in settings on the iphone 6 does not correct the problem. Not sure if its a iphone 6 issue or gmail issue.
Are you using the native Mail app or the Gmail app? If you try to check your mail using a web browser, does it also show that your incoming mail is in the trash or does it show it still in your inbox?
If you've set up Gmail correctly on your phone Gmail is still handling where your mail goes using Gmail's SMTP server, which has nothing to do with your device.
You would need to log into Gmail on the web and go to your settings - Look it over and match your settings and most of all, Make sure it is set up as IMAP. Disable POP and enable IMAP if not already . Matching up your webmail settings to your device settings should do the trick.