First of all, this occurs in Minecraft Java 1.16.3 but the affected versions will not let me enter 1.16.3. It says Version with id '1.16.3' does not exist.
The issue:
I found an issue that while in spectator mode blocks disappear.
As seen in the photo I am in spectator mode in a bedrock block in the nether. For some reason one of the blocks of the game generated portal is missing.
The block doesn't disappear, it's just that block faces are not visible when they're against another block. Since you're in spectator mode, you're able to no-clip through walls, which causes this to become visible.