I don't know if someone has reported the following bugs.
Scraptown
Several error messages in the description and dialog. Some dialog trees are messed up both on the Fools and the Blades.
When you attack the Blades with the Fools, The Queen (I don't remember the leader's name), just sputs multicoloured error messages and cannot be interacted with.
One of the Fools, black guy with metal armor has weird fonts when he speaks with you.
Vault City
When you to recruit Cassidy, you get a weird quest about bringing 6 fruit and 10 jerky to a neighboring town. The mysterious Anne may be in Cassidy's bar but dissapears if Cassidy joins your party and the bar closes down.
The prisoner liberation quest has several error lines in Steve's dialog. Some of the floting text comes up as error.
Modoc
The Cold Hearts quests are a bit buggy. Some times you can report twice to Jack and get experience twice.
The Den
Orphanage was left out (?)
Lara's quest to attack Tyler's party doesn't come up. I took a rest after hitting the church but when I came back to Lara she wouldn't offer me to hit Tyler's party.
New Reno
Taxi service works fine but when you leave the "Special Destinations" (Guardian of Forever, Cafe of Broken Dreams), the game puts you back on the coast. If you have the car at that point and you encounter something, you may lose the car as the car is "with" you but it's actually at virgin street. This happens when certain quests kick you to a different map directly (Stables or Golgotha).
Primitive Tribe
This is not so much a bug than a recommendation. The wooded area is too thick with woods. This may cause pathing issues. Sometimes the quests for the Primitive Tribe may reset and "uncomplete" themselves in the Pipboy.
Bunker 21
This location is very buggy. Almost no quests and you can deceive the general repeatedly if you keep speaking to him and picking the first line. This location needs a lot of work from the creators. The entire location "feels" as if you need to know what to do in order to get any quests. The location's requirements are bit too stiff in comparison with the overall rewards.
Vault 23
This location is very, very buggy. One of the skeletons in the third level holds a voice activated door. When you use the item you, the dialog interface opens below the inventory interface. Not only that but if you save on the last level before fighting the super rat, the map will be corrupted and you won't be able to load that game. This location feels a bit pointless as it is a mindless vault crawl with super powered rats.
Vault 13
Didn't get the option to do Vault 13 without having Franky boy visiting them afterwards. I even sent Xorn back to Vault 13 before finding the Vault itself.
Sierra Army Depot
Skynet's combat settings as a Sentry Bot are really messed up. The options selected are wrong and some are even listed as error. The NPC description appears as Robobrain or Brainbot even as a Sentry Bot. The character works however. It would be nice to add the option Be Absolutely Sure you will Not Hit Me to the burst control. Dogmeat, Goris and cyber dogs will appreciate it
One problem is the crafting items change. The problem is that having extra items to upgrade weapons will cause most player to hit the Too Many Items Bug faster than usual.
That's it for now, I haven't completed the game yet. The Megamod really makes the game feel like a new one.