diff --git a/src/spikeinterface/core/analyzer_extension_core.py b/src/spikeinterface/core/analyzer_extension_core.py
index d2dc771500..98e9e225dd 100644
--- a/src/spikeinterface/core/analyzer_extension_core.py
+++ b/src/spikeinterface/core/analyzer_extension_core.py
@@ -255,6 +255,7 @@ def _merge_extension_data(
 
         if sparsity is not None:
 
+            max_num_chans = np.sum(new_sorting_analyzer.sparsity.mask, 1).max()
             new_data["waveforms"] = waveforms.copy()
             for to_be_merged, unit_id in zip(units_to_merge, new_unit_ids):
                 new_channel_ids = sparsity.unit_id_to_channel_ids[unit_id]
@@ -263,8 +264,7 @@ def _merge_extension_data(
                 )
                 num_chans = new_waveforms.shape[2]
                 new_data["waveforms"][spike_indices, :, :num_chans] = new_waveforms
-                new_data["waveforms"][spike_indices, :, num_chans:] = 0
-
+            new_data["waveforms"] = new_data["waveforms"][:, :, :max_num_chans]
         else:
             new_data["waveforms"] = waveforms
 
diff --git a/src/spikeinterface/postprocessing/principal_component.py b/src/spikeinterface/postprocessing/principal_component.py
index e357ce9df5..fe6e842453 100644
--- a/src/spikeinterface/postprocessing/principal_component.py
+++ b/src/spikeinterface/postprocessing/principal_component.py
@@ -118,6 +118,7 @@ def _merge_extension_data(
 
         if sparsity is not None:
 
+            max_num_chans = np.sum(new_sorting_analyzer.sparsity.mask, 1).max()
             new_data["pca_projection"] = pca_projections.copy()
             for to_be_merge, unit_id in zip(units_to_merge, new_unit_ids):
                 new_channel_ids = sparsity.unit_id_to_channel_ids[unit_id]
@@ -126,7 +127,7 @@ def _merge_extension_data(
                 )
                 num_chans = new_projections.shape[2]
                 new_data["pca_projection"][spike_indices, :, :num_chans] = new_projections
-                new_data["pca_projection"][spike_indices, :, num_chans:] = 0
+            new_data["pca_projection"] = new_data["pca_projection"][:, :, :max_num_chans]
         else:
             new_data["pca_projection"] = pca_projections