Whenever I attach an alias to an item or actor now, they no longer use their scripts or dialogue. When I remove the alias the scripts and dialogue function properly, what might I be doing wrong?

Please clarify...

Not sure what you mean "attach an alias". If you make an alias called myactor that pointing to your NPC Bob, you can attach scripts to myactor that will take precedence (I believe) over the scripts that were originally given to Bob. I should think that Bob's original script should still fire when possible, unless myactor scripts are overriding them.

Why not just give the scripts to myactor instead? It's usually a cleaner method as if the quest is over those scripts won't run. If the script needs to run forever, attach them to the alias in a quest that won't end.

I too have this issue. These actors that fill an alias. are they vanilla NPCs? I'm not 100% certain, so I'm surmising a bit, but if so, many vanila NPCs may have other quests that need to use them, which may block yours. R-click and select users, to see what other quests are using them. Check the alias tab of these quests and see if the reserved flag set. I think that means that they are being held until the quests releases them. Whether you should unreserve them risks breaking the vanilla quest.

No they aren't vanilla NPCs, I created them.
Well, if I create an alias referencing my actor, they no longer will use any dialogue in game. But when I delete the alias, they use the dialogue in game. Regardless if I give dialogue to the alias or directly to the actor, it still will not work.

It happens with objects too. I created a letter and gave it a DefaultOnReadSetQuestStage script, and when I read it, it changes the quest stage in game. However, when I reference that letter with an alias, it no longer will set the stage in game.

What you should be doing is assigning the dialogue to the alias in the first place. This is a cleaner method (albeit not always suitable to your purposes). If you only require the actor to say their dialogue during your quest, then give the dialogue to the alias in the quest. So that when the quest ends, the actor won't need to (and won't ) say those dialogue lines again, making it much cleaner if you want to use the actor in another quest.

The reason they no longer use any dialogue given to their editor ID is probably because the point of the alias is to override the native dialogue topics.

How are you assigning the dialogue to the alias (you claim it doesn't work)?

I think I was using GetIsAliasRef, is that correct?

Using it for what I can't find that function n the wiki. You should put the actor in the alias and attach an actor scripting for the alias to a ReferenceAlias script. While the actor is in the alias this will have presidence over actor script.

The same goes for packages. See the wiki tutorial on this.