In Age of Ultron, we saw glimpses of Thor visiting the Water of Sight. But in the full-blown sequence, Thor revealed a major clue about the Mind Stone under Norn's possession.
Thor: Ragnarok
A post-credit scene of Ragnarok had the Grandmaster boarding the Asgardian ship Ark to reach Earth. It was deleted later, but just imagine what would have happened if it was not!
When Bruce Banner transforms into the Hulk while trying to kill himself, a giant ice structure collapses. Captain America was supposed to appear from that for a quick moment.
The Incredible Hulk
Shang-Chi
Following the release of Shang-Chi, a deleted scene was shared on Marvel's social media handles. In it, an interesting connection between the film and the first Iron Man movie was made.
Thor
We were introduced to Sentient World Observation and Response Department (S.W.O.R.D) in WandaVision. But, in the deleted ending of Thor in 2011, Dr. Erik Selvig talked about the department.