Quality gate is failed for my branch but passed for the PR raised with the same branch

SonarQube version - 10.0 (Developer Edition)
Repository - Bitbucket Cloud
SonarQube analysis triggered via Jenkins multi-branch pipeline (Branch Source Plugin and Sonar Scanner Plugin configured and put to use)

I created a new branch which has multiple bugs and vulnerabilities. The quality gate is failing which is fine but when I raise a PR with the same branch, the quality gate is passed. I need the quality gate to fail in the PR as well to prevent the merge checks.

I am using the New Code definition as “reference branch”.

Note: No new quality gates are defined. The default (Sonar way) is used for the Quality Gate analysis.

Is this in the same project as you mention here?

I have a feeling the root cause will be the same.