This only happens with Scala 3, so it could be an issue in the Scala 3 compiler, but I haven't been able to reproduce it outside of ammonite, so it might be that ammonite is doing something weird, although looking at the code of ammonite I haven't been able to pinpoint what exactly:
Welcome to the Ammonite Repl 3.0.1 (Scala 3.6.3 Java 21.0.6)
@ class Bar(); println((new Bar()).getClass.getSimpleName)
java.lang.IncompatibleClassChangeError: ammonite.$sess.cmd0 and ammonite.$sess.cmd0$Bar disagree on InnerClasses attribute
java.lang.Class.getDeclaringClass0(Native Method)
java.lang.Class.isTopLevelClass(Class.java:1971)
java.lang.Class.getSimpleBinaryName(Class.java:1956)
java.lang.Class.getSimpleName0(Class.java:1793)
java.lang.Class.getSimpleName(Class.java:1784)
ammonite.$sess.cmd0$.<clinit>(cmd0.sc:1)