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I play on an iPhone SE and have been having the same issue. Interestingly, what I have noticed is that if I'm in a call with my wife/using the gps/doing anything that puts a banner on the top ~5% of my phone screen, everything shows back up and works as you would expect.
This is to say, this is definitely a display resolution issue on Niantic's end, and it seems that iPhone 5(s/E)/iTouch screens are the only devices which have this specific display configuration. I doubt that niantic are going to patch this, as the only hardware which seems to have this issue is old and probably in need of an upgrade in 1-2 years anyway, and thus not worthy of their attention.