Ghostly skeletons causing Red dungeon alert should be fixed, as should any encounter which causes dungeon alert by design. For example, in Threnal East 3 the dormant Gargoyles used to cause Yellow dungeon alert the second you stepped in the place. This appears to have been fixed.
However, the complaints about DR mobs are going to fall on deaf ears. The DR simply prevents one type of damage - non-good physical. That's it. Your other choices are (that I can think of)
- Any elemental weapon damage
- Arcane damage spells (Magic Missile, Acid Blast, Fireball, etc.)
- Divine damage spells (Nimbus of Light, Searing Light, etc.)
- Arcane wands (any mage should have the Finger of Fire wand)
- Divine wands (any divine should have the Spark of Light wand)
- Healing spells (including Lay on Hands)
- Elemental guard items (just shield up and let them hit you)
- Undead bane
- Monk elemental damage
- Divine Light
So unless you are a party entirely composed of Maul wielding Barbarians .. you are just going to have to think on your feet.