When a job with aliases is used as a copy for a new job, the build aliases are copied over to the new project.
It might not fail immediately, but at the very least the job can't be reloaded from disk and it can't be found.
Sample from system logs include:

Failed Loading job XXXXXXXXXX (new job)
java.lang.NullPointerException
at java.util.Vector.addAll(Vector.java:880)
at hudson.model.AbstractProject.createTransientActions(AbstractProject.java:756)
at hudson.model.Project.createTransientActions(Project.java:213)
at hudson.model.AbstractProject.updateTransientActions(AbstractProject.java:749)
at hudson.model.AbstractProject.onLoad(AbstractProject.java:336)
....

Feb 09, 2014 7:03:14 PM INFO jenkins.InitReactorRunner$1 onAttained
Loaded all jobs