diff --git a/spacy/pipeline/span_finder.py b/spacy/pipeline/span_finder.py
index af4eab636..50112d692 100644
--- a/spacy/pipeline/span_finder.py
+++ b/spacy/pipeline/span_finder.py
@@ -7,7 +7,7 @@ from thinc.types import Floats2d, Ints1d, Ragged
 from spacy.language import Language
 from spacy.pipeline.trainable_pipe import TrainablePipe
 from spacy.scorer import Scorer
-from spacy.tokens import Doc
+from spacy.tokens import Doc, Span
 from spacy.training import Example
 from spacy.errors import Errors
 
@@ -160,6 +160,12 @@ class _MaxInt(int):
         return True
 
 
+def _char_indices(span: Span) -> Tuple[int, int]:
+    start = span[0].idx
+    end = span[-1].idx + len(span[-1])
+    return start, end
+
+
 class SpanFinder(TrainablePipe):
     """Pipeline that learns span boundaries"""
 
@@ -282,38 +288,52 @@ class SpanFinder(TrainablePipe):
         scores: Scores representing the model's predictions.
         RETURNS (Tuple[float, float]): The loss and the gradient.
         """
-        reference_truths = self._get_aligned_truth_scores(examples)
-        d_scores = scores - self.model.ops.asarray2f(reference_truths)
+        truths, masks = self._get_aligned_truth_scores(examples, self.model.ops)
+        d_scores = scores - self.model.ops.asarray2f(truths)
+        d_scores *= masks
         loss = float((d_scores**2).sum())
         return loss, d_scores
 
-    def _get_aligned_truth_scores(self, examples) -> List[Tuple[int, int]]:
+    def _get_aligned_truth_scores(self, examples, ops) -> Tuple[Floats2d, Floats2d]:
         """Align scores of the predictions to the references for calculating the loss"""
-        # TODO: handle misaligned (None) alignments
-        reference_truths = []
-
+        truths = []
+        masks = []
         for eg in examples:
             if eg.x.text != eg.y.text:
                 raise ValueError(Errors.E1053.format(component="span_finder"))
-            start_indices = set()
-            end_indices = set()
-
+            n_tokens = len(eg.predicted)
+            truth = ops.xp.zeros((n_tokens, 2), dtype="float32")
+            mask = ops.xp.ones((n_tokens, 2), dtype="float32")
             if self.training_key in eg.reference.spans:
                 for span in eg.reference.spans[self.training_key]:
-                    start_indices.add(eg.reference[span.start].idx)
-                    end_indices.add(
-                        eg.reference[span.end - 1].idx + len(eg.reference[span.end - 1])
+                    ref_start_char, ref_end_char = _char_indices(span)
+                    pred_span = eg.predicted.char_span(
+                        ref_start_char, ref_end_char, alignment_mode="expand"
                     )
-
-            for token in eg.predicted:
-                reference_truths.append(
-                    (
-                        1 if token.idx in start_indices else 0,
-                        1 if token.idx + len(token) in end_indices else 0,
-                    )
-                )
-
-        return reference_truths
+                    pred_start_char, pred_end_char = _char_indices(pred_span)
+                    start_match = pred_start_char == ref_start_char
+                    end_match = pred_end_char == ref_end_char
+                    # Tokenizations line up.
+                    if start_match and end_match:
+                        truth[pred_span[0].i, 0] = 1
+                        truth[pred_span[-1].i, 1] = 1
+                    # Start character index lines up, but not the end.
+                    elif start_match and not end_match:
+                        truth[pred_span[0].i, 0] = 1
+                        mask[pred_span[-1].i, 1] = 0
+                    # End character index lines up, but not the start.
+                    elif not start_match and end_match:
+                        truth[pred_span[-1].i, 1] = 1
+                        mask[pred_span[0].i, 0] = 0
+                    # Neither of them match.
+                    else:
+                        mask[pred_span[0].i, 0] = 0
+                        mask[pred_span[-1].i, 1] = 0
+            truths.append(truth)
+            masks.append(mask)
+        truths = ops.xp.concatenate(truths, axis=0)
+        masks = ops.xp.concatenate(masks, axis=0)
+        return truths, mask
 
     def _get_reference(self, docs) -> List[Tuple[int, int]]:
         """Create a reference list of token probabilities"""
diff --git a/spacy/tests/pipeline/test_span_finder.py b/spacy/tests/pipeline/test_span_finder.py
index 921601283..55d126ecc 100644
--- a/spacy/tests/pipeline/test_span_finder.py
+++ b/spacy/tests/pipeline/test_span_finder.py
@@ -63,15 +63,16 @@ def test_loss_alignment_example(tokens_predicted, tokens_reference, reference_tr
     example.reference.spans[TRAINING_KEY] = [example.reference.char_span(5, 9)]
     span_finder = nlp.add_pipe("span_finder", config={"training_key": TRAINING_KEY})
     nlp.initialize()
+    ops = span_finder.model.ops
     if predicted.text != reference.text:
         with pytest.raises(
             ValueError, match="must match between reference and predicted"
         ):
-            span_finder._get_aligned_truth_scores([example])
+            span_finder._get_aligned_truth_scores([example], ops)
         return
-    truth_scores = span_finder._get_aligned_truth_scores([example])
+    truth_scores, masks = span_finder._get_aligned_truth_scores([example], ops)
     assert len(truth_scores) == len(tokens_predicted)
-    assert truth_scores == reference_truths
+    ops.xp.testing.assert_array_equal(truth_scores, ops.xp.asarray(reference_truths))
 
 
 def test_span_finder_model():