Hello @heshambakr,
Apologies for the late response. The problem is most likely that not enough git history is being fetched. The scanner relies on the data it can find in the git history to decide what is new code in a PR and what is not. This explains why it works for you an branches (everything is scanned anyway) and not on PRs (only new code is scanned, but we can’t find any new code).
I assume you have been using the git-clone step, this optimizes the git clone step to be as fast as possible. I can’t find much documentation on this step, but it might be worth to try setting the clone_depth or the branch_dest parameter to see if this changes the behaviour.
In the worst case you can do a manual git clone, like this user did.