taginject subclasses GstBaseTransform but does not appear to be gap aware.  Given the nature of the element I assume there is no reason for it not to be gap aware and that it is simply an oversight.  I haven't tested this patch yet, but I think something like this would make it gap aware:

diff --git a/gst/debugutils/gsttaginject.c b/gst/debugutils/gsttaginject.c
index a5e78fe..e0c9d2c 100644
--- a/gst/debugutils/gsttaginject.c
+++ b/gst/debugutils/gsttaginject.c
@@ -134,6 +134,8 @@ gst_tag_inject_class_init (GstTagInjectClass * klass)
 static void
 gst_tag_inject_init (GstTagInject * self, GstTagInjectClass * g_class)
 {
+  GstBaseTransform *trans = GST_BASE_TRANSFORM (self);
+  gst_base_transform_set_gap_aware (trans, TRUE);
   self->tags = NULL;
 }