Recently I started off a new character, an Elven Ranger, now only at level 6, my henchman or rather henchwoman.. Sharwyn
I was in the crypts underneath the Great Graveyard.. Sharwyn got diseased from ghouls and later went into a room nearby. I ordered her to disable a trapped chest, she suffered fatal damage from the traps. I used the stone to teleport back to the temple, thinking she will be there but she is not!!! I took the portal back to the crypts and use the stone again to teleport back to the temple.. she is still not there!! and what's worse was that everyone became hostile and attacked me !! ...
oh.. by the way.. I had SOU installed and v1.31 patch installed.

have you guys encountered such problems?

I have heard of such problems caused by a faction bug... I would try to reload from an earlier save.