There are two ways of deleting a message in Gmail. You can delete entire thread (by using Delete button) or just one message in it:
The second delete won't be replicated in mobile Gmail. You will see this message still appearing in given thread, just as you would ever delete it. You must purge Bin folder in order to get this message delete in mobile Gmail.
Another fuckup discovered in Android... and in mindless heads of Google dev fucks.