I should start out by saying that there are some people who believe that Buddha is not an incarnation of Vishnu, and that any scriptural references to Buddha are a later interpolation. Now among the people who do believe that Buddha is an incarnation, the reason that Buddhists and Hindus have different beliefs is because of the fundamental purpose of Vishnu's incarnation as Buddha: to lead people astray from following the Vedas.
Buddha's incarnation is described in this chapter of the Vishnu Purana. The Asuras (demons) decide to engage in Tapasya (deep meditation) in accordance with Vedic principles, and as a result the gods unable to harm them, so they turn to Vishnu to help. Vishnu incarnates as Buddha in order to lead the Asuras astray from the teachings of the Vedas, so that the gods could defeat them in battle:
After this, the great delusion, having proceeded to earth, beheld the Daityas engaged in ascetic penances upon the banks of the Narmadá river; and approaching them in the semblance of a naked mendicant, with his head shaven, and carrying a bunch of peacock's feathers 2, he thus addressed them[.]... By such persuasions, and by many specious arguments, did this delusive being mislead the Daityas from the tenets of the Vedas; teaching that the same thing might be for the sake of virtue and of vice; might be, and might not be; might or might not contribute to liberation; might be the supreme object, and not the supreme object; might be effect, and not be effect; might be manifest, or not be manifest; might be the duty of those who go naked, or who go clothed in much raiment[.]...
Then the same deluder, putting on garments of a red colour, assuming a benevolent aspect, and speaking in soft and agreeable tones, addressed others of the same family, and said to them, "If; mighty demons, you cherish a desire either for heaven or for final repose, desist from the iniquitous massacre of animals (for sacrifice), and hear from me what you should do. Know that all that exists is composed of discriminative knowledge. Understand my words, for they have been uttered by the wise. This world subsists without support, and engaged in the pursuit of error, which it mistakes for knowledge, as well as vitiated by passion and the rest, revolves in the straits of existence." In this manner, exclaiming to them, "Know!" (Budhyadwam), and they replying, "It is known" (Budhyate), these Daityas were induced by the arch deceiver to deviate from their religious duties (and become Bauddhas), by his repeated arguments and variously urged persuasions, When they had abandoned their own faith, they persuaded others to do the same, and the heresy spread, and many deserted the practices enjoined by the Vedas and the laws.
So the reason the followers of an incarnation of a Vedic god like Vishnu could deny the Vedas would be that Vishnu intentionally spread doctrines that were contrary to the Vedas. And insofar as Hindus believe that the truths embodied in the Vedas are of divine origin, there is naturally a divergence in the beliefs of Hindus and Buddhists.