IF there is in fact a tendency for Pluto to show in the 12th house in your various charts then this IS something the Cosmos is trying to point out to you: Pluto represents (among other significations) deep and hidden energies, and coupled with th 12th house (same thing! and also other indications relating to personality, etc) there is likely a pointing to those types of forces playing an important role for you.
So, no, if there is such a tendency by no means ignore it-quite the opposite: investigate it!!