According to IGN, this was intentional.
The end credits scene of Venom introduces serial killer Cletus Kasady, played by Woody Harrelson, in a clear set-up for the introduction of the villain Carnage in a potential sequel.
Director Ruben Fleischer recently sat down for a one-on-one spoiler chat with IGN wherein he discussed the casting of Harrelson and his reasons for why Carnage wasn't used as the villain of the first Venom movie.
Fleischer explained that the priority of the first movie was to establish Eddie Brock and his bond with the symbiote Venom -- "their relationship is really the most satisfying part of the movie" -- and that the inclusion of Cletus Kasady was only meant to whet fans' appetites for a sequel.
"We’d like to think that this movie will expand to other movies and Carnage is, I think, the most beloved of the Venom adversaries, with the exception of probably Spider-Man," Fleischer said. "And so we definitely didn’t want to include Carnage in this first movie because it felt like we wanted to establish Eddie and Venom and so that’s why we worked having Riot as our main adversary. But the intention or the ambition was to show that there are legs for the franchise in that a fan favorite let alone played by Woody Harrelson would be something we could look forward to in the future."
Why did they end up deleting Carnage's scenes - and since they ended up getting deleted, why did they begin shooting with Carnage in the first place?
I cannot find any explicit mention on this. However, it's not that uncommon for some additional things to be shot without already having confirmed that it will actually be included.