In case of the Black Morass (Opening the Dark Portal), each party member can and should pick up the Chrono Beacon from the NPC at the cave entrance in the dungeon (Sa’at), if you wish to make it a bit easier. Just use it when you feel that you need some extra help - so most likely on the last boss.
In other cases it is mostly matter of the specific boss mechanic. In Manatombs even 1st boss is able to wipe the party if the DPS will not stop on the phase when he redirects damage back.
Arcatraz is a very good example of one of the most complex dungeons from that expansion. However I would say that each part of the Tempest Keep area dungeon complex had some quite challenging mechanics for their bosses. Scrooloose did summarize the Arcatraz encounters pretty well.
That being said, it is still possible for some bugs to happen with scaling or other factors. If you do see any problem like this, you are more than welcome to report it in game (Esc → Help → Submit Bug). This will help our game developers to track it down and fix it rather sooner than later.