Is saying "may it be accepted" to someone who has returned from Mecca considered a bid'ah (innovation) that could lead to disbelief?

There is nothing wrong with what was said to your friend, as it falls under the category of optimism and supplicating for him that his 'Umrah (definition) be accepted. This is indeed recommended, as mentioned by scholars. It has been reported from Imam Ahmad, Ibn 'Umar, and others that it is recommended to supplicate for the pilgrim (Haji) and the 'Umrah performer that their pilgrimage be accepted and that they be forgiven.