I recently bought my xperia z3 about-two days ago-however since then I've noticed the flap for the micro SD and nano sim sticks out a little more than the flap for the micro USB connector. You can feel the difference as you slide your finger atop both the flaps with the micro USB one being more flushed in with the design and hardly noticeable whereas the other one has a very small difference and stands out a little more and I'm not sure of it is actually broken or not which would definitely affect waterproofing if it is broken which is what I'm worried about, all answers are much appreciated 
