Bad writing mostly.
Nobody noticed the Oil Tanker dock at the Oil Rig even though the Enclave specifically disabled the tanker themselves because they knew it was a threat? President Richardson doesn't raise the alarm when you openly declare yourself to be an enemy infiltrator to his face? All the prisoners held in the holding cells on the Oil Rig manage to sneak back through the Rig to the Tanker without getting caught?
Enclave doesn't use the artillery in Fallout 3 that they use to shell the bridge in-front of the Pentagon on the Pentagon itself? Enclave never uses Bradley-Hercules on the Pentagon even though it's entirely capable of firing?
The Enclave were basically made too powerful if anything and have been in every iteration so it just requires hand waving to beat them.