If an embedded entity use a circular dependency, the example is Company{Employee[]} Employee{Company} the invocation of put will end in a stack overflow.
It does not matter whether the Marshalling is done with custom Marshaller or the @AutoProtoSchemaBuilder is used.

Error with @AutoProtoSchemaBuilder

java.lang.reflect.InvocationTargetException
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:566)
    at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:293)
    at java.lang.Thread.run (Thread.java:829)
Caused by: java.lang.StackOverflowError
    at org.infinispan.protostream.impl.TagWriterImpl$OutputStreamNoBufferEncoder.writeVarint32 (TagWriterImpl.java:728)
    at org.infinispan.protostream.impl.TagWriterImpl$Encoder.writeUInt32Field (TagWriterImpl.java:303)
    at org.infinispan.protostream.impl.TagWriterImpl.writeInt32 (TagWriterImpl.java:138)
    at org.infinispan.wfink.playground.ickle.hotrod.domain.Company$__Marshaller_122420a9663802783129e8afc10a8c94510b1eadac2a59113d3afcfc2c5eb858.write (Company$__Marshaller_122420a9663802783129e8afc10a8c94510b1eadac2a59113d3afcfc2c5eb858.java:112)
    at org.infinispan.wfink.playground.ickle.hotrod.domain.Company$__Marshaller_122420a9663802783129e8afc10a8c94510b1eadac2a59113d3afcfc2c5eb858.write (Company$__Marshaller_122420a9663802783129e8afc10a8c94510b1eadac2a59113d3afcfc2c5eb858.java:15)
    at org.infinispan.protostream.impl.ProtobufTagMarshallerDelegate.marshall (ProtobufTagMarshallerDelegate.java:27)
    at org.infinispan.protostream.annotations.impl.GeneratedMarshallerBase.writeMessage (GeneratedMarshallerBase.java:33)
    at org.infinispan.protostream.annotations.impl.GeneratedMarshallerBase.writeNestedMessage (GeneratedMarshallerBase.java:43)
    at org.infinispan.wfink.playground.ickle.hotrod.domain.Employee$__Marshaller_889ea1c1f15d1245561a51233659a97474058a605ce5882698073ad951204a79.write (Employee$__Marshaller_889ea1c1f15d1245561a51233659a97474058a605ce5882698073ad951204a79.java:132)
    at org.infinispan.wfink.playground.ickle.hotrod.domain.Employee$__Marshaller_889ea1c1f15d1245561a51233659a97474058a605ce5882698073ad951204a79.write (Employee$__Marshaller_889ea1c1f15d1245561a51233659a97474058a605ce5882698073ad951204a79.java:15)
    at org.infinispan.protostream.impl.ProtobufTagMarshallerDelegate.marshall (ProtobufTagMarshallerDelegate.java:27)
    at org.infinispan.protostream.annotations.impl.GeneratedMarshallerBase.writeMessage (GeneratedMarshallerBase.java:33)
    at org.infinispan.protostream.annotations.impl.GeneratedMarshallerBase.writeNestedMessage (GeneratedMarshallerBase.java:43)
    at org.infinispan.wfink.playground.ickle.hotrod.domain.Company$__Marshaller_122420a9663802783129e8afc10a8c94510b1eadac2a59113d3afcfc2c5eb858.write (Company$__Marshaller_122420a9663802783129e8afc10a8c94510b1eadac2a59113d3afcfc2c5eb858.java:126)
    at org.infinispan.wfink.playground.ickle.hotrod.domain.Company$__Marshaller_122420a9663802783129e8afc10a8c94510b1eadac2a59113d3afcfc2c5eb858.write (Company$__Marshaller_122420a9663802783129e8afc10a8c94510b1eadac2a59113d3afcfc2c5eb858.java:15)
    at org.infinispan.protostream.impl.ProtobufTagMarshallerDelegate.marshall (ProtobufTagMarshallerDelegate.java:27)
    at org.infinispan.protostream.annotations.impl.GeneratedMarshallerBase.writeMessage (GeneratedMarshallerBase.java:33)
    at org.infinispan.protostream.annotations.impl.GeneratedMarshallerBase.writeNestedMessage (GeneratedMarshallerBase.java:43)
    at org.infinispan.wfink.playground.ickle.hotrod.domain.Employee$__Marshaller_889ea1c1f15d1245561a51233659a97474058a605ce5882698073ad951204a79.write (Employee$__Marshaller_889

Error with dedicated Marshaller implementation:

java.lang.reflect.InvocationTargetException
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at jdk.internal.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:566)
    at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:293)
    at java.lang.Thread.run (Thread.java:829)
Caused by: java.lang.StackOverflowError
    at org.infinispan.protostream.impl.TagWriterImpl.getProtoStreamWriter (TagWriterImpl.java:283)
    at org.infinispan.protostream.impl.TagWriterImpl.getProtoStreamWriter (TagWriterImpl.java:283)
    at org.infinispan.protostream.impl.TagWriterImpl.getProtoStreamWriter (TagWriterImpl.java:283)