I've never been a particular fan of pet classes (except PUP) and so haven't taken one to dungeons yet but I have noticed others having this issue.
The morbol fruit one seems like a simple oversight that should be fixed easily. I think perhaps that in certain circumstances pets should benefit from whatever damage mitigation the player has. As to the positioning of pets I agree something needs to be done but hopefully when they fix it they don't over fix it. I have seen several sch/smn allowing their pets to suffer unnecessary damage simply by not staying aware of their position. Often they will stand just outside an aoe marker leaving their pet inside or I've even seen them run across an aoe marker trailing their pet inside and leaving it there.