Bludgeoning weapons that have extra bludgeoning damage do not gain increased damage from magic weapon spell. Might be true for slashing and pierceing as well, I don't know.

Animated party members take damage from Negative energy traps.

The option to rest at Thomas' undeath shop is taken away if you complete the quest for him.

These aren't bugs, increased damage already on a weapon is still increased damage. Now Magic weapon gives you the chance to Bypass DR and increases BY by one.

NEgative energy damage on weapons harms undead, why not traps?

Don't know about three.

I must admit i have always found it odd that a negative energy trap harms/damages undead it's contrary to everything written in cannon so i can't quite work that one out myself is it a bug or not?

Also 3 is true i know from experience