Remove certain commits from history in a git branch

Let's visualize your scenario:

o---o (main)
     \
      A---B (A)
           \
            C---D (B)

In Git, a branch is simply a reference to the latest of a sequence of commits. What commits are in a branch depends on which branches you're comparing:

• If you compare A with main, then A has commits A and B which main doesn't have.
• If you compare B with A, then B has commits C and D which main doesn't have.
• If you compare B with main, then B has commits A, B, C and D which main doesn't have.

Now, if branch A were to be merged into main, then main would also have commits A and B. This means that if you compare branch B with main after the merge, then B would have commits C and D that aren't in main:

o---o-------M (main)
     \     /
      A---B (A)
           \
            C---D (B)  <-- these commits aren't in 'main'

The fact that GitHub is showing you commits from branch A when you do a pull request from branch B to main makes me think that branch A was rewritten (possibly rebased) after you created branch B:

o---o---o--------M (main)
     \   \      /
      \   A'---B' (A)      <-- rebased commits in branch 'A'
       \ 
        A---B---C---D (B)  <-- branch 'B' still has the old commits

If this is indeed the case, the solution is simply to rebase branch B on top of main and update the pull request:

o---o---o--------M (main)
         \      / \
          A'---B'  \
               ^    \
              (A)    C---D (B)

Git will notice that the changes from commits A and B are already in main thanks to commits A' and B' and will therefore only show you commits C and D when you compare branch B to main.