With the attached minimized two yang modules the following error message is printed:

my-model-1:
[main] WARN org.opendaylight.yangtools.yang.parser.stmt.reactor.BuildGlobalContext - Unexpected error processing source RevisionSourceIdentifier [name=my-model-1@1970-01-01]. Please file an issue with this model attached.
java.lang.IllegalArgumentException: Refine target node Relative

{path=[(my-model-1-ns?revision=1970-01-01)my-grouping-container]}

not found. At null:16:6

my-model-2:
[main] ERROR org.opendaylight.yangtools.yang.parser.stmt.reactor.BuildGlobalContext - Failed to parse YANG from source SourceSpecificContext [source=null, current=EFFECTIVE_MODEL, finished=FULL_DECLARATION]: Augment target 'Relative

{path=[(my-model-2-ns?revision=1970-01-01)my-container, (my-model-2-ns?revision=1970-01-01)my-grouping-container]}

' not found [at null:18:2]

The full stacktraces are available inside the attachment.

Tested with released version 1.0.4-Boron-SR4.