The story of Daksha's Yajna, Devi Sati's demise is quite well known.
When Lord Shiva received the news of Sati's demise he was furious and he created out of himself a terrifying demon called "Virabhadra".
And Virabhadra did defeat Lord Vishnu and his powerful weapon, the Sudarshana Chakra.
Quoting the relevant portions from the Kurma Purana:
Virabhadra had a thousand heads, a thousand feet, a thousand eyes and
a thousand arms. His body shone with radiance like the sun at the time
of destruction. The thousand arms held all sorts of weapons in them.
“What are my orders?” Virabhadra asked Shiva.
“Go and destroy Daksha’s yajna,” was the reply.
Virabhadra ascended a bull and set out for Daksha’s house. He created
thousands and thousands of demons who would aid him in the task of
destruction. These demons were armed with spears, tridents, maces,
clubs and stones. Parvati also created a goddess named Bhadrakali who
would help Virabhadra.........
Vishnu himself came to intervene and Virabhadra began to fight with
Vishnu has a wonderful weapon named sudarshana chakra (a
bladed-discuss) and he hurled this at Virabhadra. But Virabhadra
easily repelled this weapon with his arrows. Vishnu is carried by
Garuda, king of the birds. Garuda attacked Virabhadra, but so fierce
was Virabhadra, that Garuda had to flee. The entire universe marvelled
to see that Virabhadra could thus vanquish Vishnu and Garuda.
So,this incident records one failure of the Sudarsana Chakra.
Edit- Adding yet another incident where Vishnu's weapons (including the Sudarshana Chakra) failed.
This incident is mentioned in the Linga Purana where Rishi Dadhichi proves the superiority of Shiva-Shakti to king Ksupa. You should read the whole story from the above link. I'm quoting below only the relevant portions from that page.
Brahma’s son King Kshupa and Maha Muni Dadhichi the son of Maharshi
Chyavana were good friends but got entangled in an argument whether
Kshatriyas were superior to Brahmanas......
As Dadhici accomplished indestructibility of his bones thanks to his
exemplary devotion to Parama Shiva, the Muni retaliated King Kshupa
and hit him hard when the latter remembered Vishnu and prayed to him
As Bhagavan appeared before the King who was a life -long Bhakta of
his, the King narrated the entire background as to how he was insulted
and humbled and requested Vishnu that Dadhichi the invincible due to
his devotion to Shiva had turned arrogant and hence must be taught a
lesson. Vishnu assumed the form of a Brahmana and sought a boon from
Dadhichi, the Shiva Bhakta. As Dadhichi had the powers of recognition,
he recognised Vishnu and a smiling Vishnu complimented the Muni and
stated that since the Muni was a Shiva Bhakta he should be afraid of
nothing including Vishnu. As Dadhichi asserted so and even
belittlled Vishnu; Vishnu grew angry with the brazen and bold
behaviour of the Muni, and got ready to fight; as Vishnu readied
to instruct his Sudashana Chakra, Dadhichi joked that Shiva gifted the
Chakra and thus would not hurt a Shiva Bhakta and similarly Brahmastra
would not work anyway. Vishnu got furious and tried various other
Astra-Shastras but Dadhichi used Kusha grass tops and the Vishnu’s
Astras proved ineffective. As a final resort Vishnu spread his Maya
and created crores of his own Swarupas, crores of Devas and of Munis.
Dadhichi shouted on Vishnu, ‘Lord! Please do not utilise your old
tricks of Vishnu Maya on me but instead look at me as Parama Shiva in
whose body you could vision every body including yourself and the
entire ‘Brahmanda’. As Dadhichi said so, Devatas got frightened and
flew away and Vishnu became still and motionless! Dadhichi then cursed
Devas for their deeds against him and forewarned them that at the time
of Daksha Yagna in the future, Rudra Deva would teach a lesson to all
including Vishnu! As the Maharshi said this and returned to his
‘Ashram’, everybody including Brahma and Devas, let alone the King
Kshupa followed him and paid respects to him and that Place came to
be famed as Sthaaneshwara there after.