It's almost always judgement calls. Same as holds and many other non-procedure penalties. Holding happens a lot more than it's called, but it doesn't generally effect the play, so it isn't called. Some calls just get missed; pointing to a singular play in one game as an example of not understanding PI may be doing yourself some injustice; it seems like you know what PI is, just that it was a missed call in that game.
As far as good coverage is concerned, there is hand fighting when going up for passes, as WR and DB. I think generally as long as the contact is kept to hands, it doesn't get called. If you're draping an arm, or if you are impeding the WRs path, it's gonna get called. Contact with the bicep, without seeing it, may be inconsequential. The contact with the hand/wrist is somewhat to be expected.