If a UProperty that stores a reference to an asset is deleted, the reference to that asset lingers in any Blueprints that had a reference stored in that UProperty. This can lead to issues when the referenced asset is altered/deleted. The reference also shows in the Reference viewer.
This also occurred in 4.14
Workaround: Move any affected blueprints to another folder and then move them back, the reference will disappear.
Head over to the existing AnswerHub thread and let us know what's up.