Personally, I wouldn't get too worked up about finding a plastic box in my room. It's not worth the stress. Just tell your roommate not to enter your room again.
Now finding dog crap or a trashed apartment is something that would annoy me to no end. I think that you and your roommate need to clearly state the guidelines to living peacefully. If you or your guests or your pet make a mess, clean it up. That's not too much to expect.
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