Nope. Per the MM, a lycanthrope receives Con bonuses to the animal hit dice for the animal-form Con, and all other hit dice for the non-animal-form Con. "For example, a human commoner with a Constitution score of 11 as a human and a Constitution score of 15 as a wolf has 1d4 plus 2d8+4 hit points." Makes things a little simpler if the PC isn't constantly changing HP.
Note also that "extra hit points" is strictly defined. "Extra hit points" can be gained from several sources (the Aid spell, vampiric weapons, bardic Inspire Greatness), but Con increases raise your "base" HP and are not considered "extra". The big difference is "extra" HP are lost "first", whereas increases to "base" HP are effectively lost last.
Example: Bob the fighter is 10th level and has 100 HP. He drinks a potion of Bear's Endurance, raising his Con modifier by +2. His "base" HP are now 120. Then the party cleric casts Aid on him, giving him 15 "extra" HP for a total of 135. Bob wades into combat and takes 45 damage total: the first 15 are applied to his "extra" HP, the other 30 to his "base". His current HP total is now 90. A little while later the Aid wears off: Bob's HP are still 90 (120 - 30). Some time later the Bear's Endurance wears off: Bob's HP are now 70 (100 - 30). If Bob had taken 110 damage in that combat, he'd better get some healing or he'll die when the Con increase wears off.