Badrayana/Vyasa refuted the Bhagavata view yet Mahabharata contains Pancharatra tradition passing down, as well as a Pancharatra scripture, Vyasa refers back to Bhagavad Gita too, which is also considered as a Pancharatra/Vaishnava scripture. Why is it so?
First of all, you're right that the Bhagavad Gita is part of the Pancharatra tradition. Here is what this chapter of the Shanti Parva of the Mahabharata, which describes how the Pancharatra tradition was passed down, says:
During the seventh birth of Brahma due to the lotus, O king, that sprang from the navel of Narayana, this cult was once more declared by Narayana himself, unto the Grandsire of pure soul, the Creator of all the worlds, in the beginning of this Kalpa. The Grandsire gave it in days of yore to Daksha (one of his sons created by a fiat of his will). Daksha, in his turn, imparted it to the eldest of all the sons of his daughters, O monarch, viz., Aditya who is senior in age to Savitri. From Aditya, Vivaswat obtained it. In the beginning of the Treta Yuga, Vivaswat imparted the knowledge of this cult to Manu. Manu, for the protection and support of all the worlds, then gave it to his son Ikshaku. Promulgated by Ikshaku, that cult over-spreads the whole world. When the universal destruction comes, it will once more return to Narayana and be merged in Him. The religion which is followed and practised by the Yatis, has, O best of kings, been narrated to thee before this in the Hari Gita, with all its ordinances in brief. The celestial Rishi Narada got it from that Lord of universe, viz., Narayana himself, O king, with all its mysteries and abstract of details. Thus, O monarch, this foremost of cults is primeval and eternal. Incapable of being comprehended with ease and exceedingly difficult of being practised, it is always upheld by persons wedded to the attribute of Sattwa.
The Hari Gita is another name for the Bhagavad Gita, and as the passage says it encapsulates the teachings of Pancharatra.
In any case, yes, it would be odd if Vyasa, who praises Pancharatra in the Mahabharata, were to criticize them in the Brahma Sutras. But not everyone believes that Vyasa criticizes them in the Brahma Sutras. Adi Shankaracharya believed that, but other commentators disagree as you can see here. Ramanujacharya believed that Vyasa actually defended Pancharatra in the Brahma Sutras, and he cites the Mahabharata to demonstrate Vyasa's support for Pancharatra. Here is what Ramanujacharya says in this section of the Sri Bhashya:
The author of the Sûtras (Vyâsa)--who first composed the Sûtras, the purport of which it is to set forth the arguments establishing the Vedânta doctrine, and then the Bhârata-samhitâ (i.e. the Mahâbhârata) in a hundred thousand slokas in order to support thereby the teaching of the Veda--himself says in the chapter called Mokshadharma, which treats of knowledge, 'If a householder, or a Brahmakârin, or a hermit, or a mendicant wishes to achieve success, what deity should he worship?' and so on; explains then at great length the Pañkarâtra system, and then says, 'From the lengthy Bhârata story, comprising one hundred thousand slokas, this body of doctrine has been extracted, with the churning-staff of mind, as butter is churned from curds--as butter from milk, as the Brahmana from men, as the Âranyaka from the Vedas, as Amrita from medicinal herbs.--This great Upanishad, consistent with the four Vedas, in harmony with Sânkhya and Yoga, was called by him by the name of Pañkarâtra. This is excellent, this is Brahman, this is supremely beneficial. Fully agreeing with the Rik, the Yagus, the Sâman, and the Atharvân-giras, this doctrine will be truly authoritative.' The terms Sânkhya and Yoga here denote the concentrated application of knowledge and of works. As has been said, 'By the application of knowledge on the part of the Sânkhya, and of works on the part of the Yogins.' And in the Bhîshmaparvan we read, 'By Brahmanas, Kshattriyas, Vaisyas and Sûdras, Mâdhava is to be honoured, served and worshipped--he who was proclaimed by Sankarshana in agreement with the Sâtvata law.'--How then could these utterances of Bâdarâyana, the foremost among all those who understand the teaching of the Veda, be reconciled with the view that in the Sûtras he maintains the non-authoritativeness of the Sâtvata doctrine, the purport of which is to teach the worship of, and meditation on, Vâsudeva, who is none other than the highest Brahman known from the Vedânta-texts?