That is a very common glitch as it's been around for ages - I'm not even sure if I remember a time where it did not happen, though it's certainly more frequent now than in the past.
Rest assured it usually fixes itself once you change location. It usually only happens to one pirate at a time (you may not be able to walk in to the zone, but others can) and a simple teleport from and back to an island or a server change usually fixes it
