From the little I know, it seems that the club felt that the supporters trust was doing too much community work and not enough directly for the club (therefore somewhat ironic they formed the Community Trust). I believe the Mongolian trip and associated fundraising is particularly frowned upon.
Regardless of this, both sides need to come together as we are far too small a club to be split. I have no axe to grind with Paul H but there are some fantastic people on the supporters trust with nothing but the club at heart.
Can't be bothered too look for it to post but Tranmere chairman Mark Palios did a great interview after their play off win highlighting the importance of the fans