It's not clear whether it's an error if an element with a type Reference and an aggregationMode of "contained" or "bundled" is present but doesn't actually have a "reference/@value" that resolves. For example, is it legal to do this:

1.
<subject><display value="foo"/></subject>

or

2.
<subject><reference><extension url="...whatever"><valueString value="foo"/></extension></reference></subject>

I see three possibilities:
a) If the aggregation mode is "contained" or "bundled", then it must always resolve to a resource that's either contained or in the same bundle. (So both #1 and #2 are errors)

b) If the aggregation mode is "contained" or "bundled" AND the Reference.reference element is present, then it must resolve to a resource that's either contained or in the same bundle. (So #1 is fine, but #2 is an error)

c) Aggregation mode is only relevant if the Reference.reference.value element is present. (So both #1 and #2 are fine.)