Well, it may help to know that after I put a robber screen on my hive, there were lots of bees just hanging around constantly for a couple of weeks. After a while it subsided. I would guess that you still have hopeful robbers hanging around. Your hive bees won't have any trouble getting in and out of the screen. I was worried about the same thing, until I watched for a while and started to notice how some bees (mine) found their way in immediately, while others (robbers) hovered and crawled around poking at any spot that looked like it might be an opening.
For the inner cover, Gypsi showed me how to roll up a bit of metal screening and stuff it in the inner cover hole -- it's a lot harder for robbers to push that in. You might try that, it worked perfectly for me. After a little while my bees glued it solidly in place so it wouldn't move at all.
Not sure what to do about the bees in the top, since you can't leave it open while feeding. They may just have to die in there. Anyway, they probably aren't your bees anyway -- your bees wouldn't be hunting for weird ways into the hive, they already know where the entrance is.