Possibly similar to JENKINS-59546:

I have a project with a Jenkinsfile containing a declarative pipeline in a git repository that also has submodules. I have activated submodule processing, and submodules are initialized correctly, but cloning them fails with a login error from the ssh connection opened by git.

It seems that multiple keys are tried (I get two "Permission denied" messages), although credentials config inside the project explicitly specifies which key to use.