diff --git a/spacy/pipeline/entity_linker.py b/spacy/pipeline/entity_linker.py
index 89e7576bf..12c3e382f 100644
--- a/spacy/pipeline/entity_linker.py
+++ b/spacy/pipeline/entity_linker.py
@@ -234,10 +234,11 @@ class EntityLinker(TrainablePipe):
         nO = self.kb.entity_vector_length
         doc_sample = []
         vector_sample = []
-        for example in islice(get_examples(), 10):
-            doc = example.x
+        for eg in islice(get_examples(), 10):
+            doc = eg.x
             if self.use_gold_ents:
-                doc.ents = example.y.ents
+                ents, _ = eg.get_aligned_ents_and_ner()
+                doc.ents = ents
             doc_sample.append(doc)
             vector_sample.append(self.model.ops.alloc1f(nO))
         assert len(doc_sample) > 0, Errors.E923.format(name=self.name)
@@ -312,7 +313,8 @@ class EntityLinker(TrainablePipe):
 
         for doc, ex in zip(docs, examples):
             if self.use_gold_ents:
-                doc.ents = ex.reference.ents
+                ents, _ = ex.get_aligned_ents_and_ner()
+                doc.ents = ents
             else:
                 # only keep matching ents
                 doc.ents = ex.get_matching_ents()
@@ -345,7 +347,7 @@ class EntityLinker(TrainablePipe):
         for eg in examples:
             kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
 
-            for ent in eg.reference.ents:
+            for ent in eg.get_matching_ents():
                 kb_id = kb_ids[ent.start]
                 if kb_id:
                     entity_encoding = self.kb.get_vector(kb_id)
@@ -356,7 +358,11 @@ class EntityLinker(TrainablePipe):
         entity_encodings = self.model.ops.asarray(entity_encodings, dtype="float32")
         selected_encodings = sentence_encodings[keep_ents]
 
-        # If the entity encodings list is empty, then
+        # if there are no matches, short circuit
+        if not keep_ents:
+            out = self.model.ops.alloc2f(*sentence_encodings.shape)
+            return 0, out
+
         if selected_encodings.shape != entity_encodings.shape:
             err = Errors.E147.format(
                 method="get_loss", msg="gold entities do not match up"
diff --git a/spacy/tests/pipeline/test_entity_linker.py b/spacy/tests/pipeline/test_entity_linker.py
index 83d5bf0e2..ccf26f890 100644
--- a/spacy/tests/pipeline/test_entity_linker.py
+++ b/spacy/tests/pipeline/test_entity_linker.py
@@ -14,7 +14,7 @@ from spacy.pipeline.legacy import EntityLinker_v1
 from spacy.pipeline.tok2vec import DEFAULT_TOK2VEC_MODEL
 from spacy.scorer import Scorer
 from spacy.tests.util import make_tempdir
-from spacy.tokens import Span
+from spacy.tokens import Span, Doc
 from spacy.training import Example
 from spacy.util import ensure_path
 from spacy.vocab import Vocab
@@ -1075,3 +1075,32 @@ def test_no_gold_ents(patterns):
 
     # this will run the pipeline on the examples and shouldn't crash
     results = nlp.evaluate(train_examples)
+
+@pytest.mark.issue(9575)
+def test_tokenization_mismatch():
+    nlp = English()
+    # include a matching entity so that update isn't skipped
+    doc1 = Doc(nlp.vocab, words=["Kirby", "123456"], spaces=[True, False], ents=["B-CHARACTER", "B-CARDINAL"])
+    doc2 = Doc(nlp.vocab, words=["Kirby", "123", "456"], spaces=[True, False, False], ents=["B-CHARACTER", "B-CARDINAL", "B-CARDINAL"])
+
+    eg = Example(doc1, doc2)
+    train_examples = [eg]
+    vector_length = 3
+
+    def create_kb(vocab):
+        # create placeholder KB
+        mykb = KnowledgeBase(vocab, entity_vector_length=vector_length)
+        mykb.add_entity(entity="Q613241", freq=12, entity_vector=[6, -4, 3])
+        mykb.add_alias("Kirby", ["Q613241"], [0.9])
+        return mykb
+
+    entity_linker = nlp.add_pipe("entity_linker", last=True)
+    entity_linker.set_kb(create_kb)
+
+    optimizer = nlp.initialize(get_examples=lambda: train_examples)
+    for i in range(2):
+        losses = {}
+        nlp.update(train_examples, sgd=optimizer, losses=losses)
+
+    nlp.add_pipe("sentencizer", first=True)
+    results = nlp.evaluate(train_examples)