When I was in Ivarstead for the first time I cleared out Geirmund's Hall. Now when I'm trying to get through the Forbidden Legend quest and finding all the amulet pieces the Geirmund's Hall part of the quest doesn't seem to trigger or work properly. When I went in there a second time the area respawned, but instead of finding Sigdis Gaulderson as the final boss (like I did the first time, when he didn't carry part of the amulet) there was a relatively powerful draugr, which didn't carry part of the amulet. Following the quest marker it lead to a point in the final chamber in the water, no amulet in sight. I used the no clip console command and I still couldn't find it anywhere.

Are bugs like these common? Is there a way to fix this? It's seems a little odd that Bethesda doesn't expect some people to clear out a dungeon before they need to for a quest.

Yes it is common. The problem is not as simple as it sounds. (The items are being created, but being "saved"/"sent", to the wrong data-slot.)

EG, it is creating the item, but placing the item into another "thing"... Might show as an extra bunny in your game, or a backwards flying dragon, or a cloned NPC, or a fruit-bowl that constantly re-appears in your inventory, no matter how many times you sell it.. of it might just make it start raining, or turn all citizens in Riverwood into aggressive for your personal enjoyment, next time you visit.

You will see it more, now that you have seen it once... The corruption grows until the game is no longer playable.

Add it to the official bugs-list, but realize that "This is the result of another bug, not an actual bug in this quest." It could have been any previous interaction that caused this item to be placed in another location. Like an ash-pile that "thinks it is gone", but still lingers in the Data, at the cell where the target should have been written, so it would draw in that cave, for that quest...

NOTE: The best luck I have had with "spawn related" quests like this... Save before talking to anyone. Talk to them, try to do the quest... if the item isn't there. Reload that save, and ask again. Seems that you can reload the same game over and over, and things change... Things that shouldn't... Resulting in the game possibly "spawning correctly", when other times it "spawns incorrectly".

Perfect example of this, is saving the game after sneaking past the bear in the beginning of the game, with your follower waiting for you just before the exit to the game. Go back and save the game when you are near the bear in the cave. Let him see you and attack... He will kill you. Reload that spot in the game... Now the bear won't hurt you at all. He will hit you, your health will go down like 1 point, and you will heal 2 points... Load it again, and he will be able to kill you again, doing 15 points per swing... Load it again... Pure random roll of the dice... Eventually he will turn into "Sigdis Gaulderson".. JK.. But he could!