diff --git a/deeptrack/models/gnns/generators.py b/deeptrack/models/gnns/generators.py
index 73a08b1ba..952412e88 100644
--- a/deeptrack/models/gnns/generators.py
+++ b/deeptrack/models/gnns/generators.py
@@ -116,7 +116,7 @@ class ContinuousGraphGenerator(ContinuousGenerator):
     the speed gained from reusing images. The generator will continuously
     create new trainingdata during training, until `max_data_size` is reached,
     at which point the oldest data point is replaced.
-    
+
     Parameters
     ----------
     feature : dt.Feature
@@ -153,9 +153,9 @@ def __getitem__(self, idx):
         batch, labels = super().__getitem__(idx)
 
         # Extracts minimum number of nodes in the batch
-        cropNodesTo = np.min(
-            list(map(lambda _batch: np.shape(_batch[0])[0], batch))
-        )
+        numofnodes = list(map(lambda _batch: np.shape(_batch[0])[0], batch))
+        bgraph_idx = np.argmin(numofnodes)
+        cropTo = int(numofnodes[bgraph_idx])
 
         inputs = [[], [], [], []]
         outputs = [[], [], []]
@@ -166,26 +166,28 @@ def __getitem__(self, idx):
 
             # Clip node features to the minimum number of nodes
             # in the batch
-            nodef = batch[i][0][:cropNodesTo, :]
-
-            last_node_idx = 0
-            # Extracts index of the last node in the adjacency matrix
-            try:
-                last_node_idx = int(
-                    np.where(batch[i][2][:, 1] <= cropNodesTo - 1)[0][-1] + 1
+            nodef = batch[i][0][:cropTo, :]
+
+            edge_dropouts = (
+                np.any(batch[i][2] > cropTo - 1, axis=-1)
+                if i != bgraph_idx
+                else np.array(
+                    [
+                        False,
+                    ]
+                    * np.shape(batch[i][2])[0]
                 )
-            except IndexError:
-                continue
+            )
 
             # Clips edge features and adjacency matrix to the index
             # of the last node
-            edgef = batch[i][1][:last_node_idx]
-            adjmx = batch[i][2][:last_node_idx]
-            wghts = batch[i][3][:last_node_idx]
+            edgef = batch[i][1][~edge_dropouts]
+            adjmx = batch[i][2][~edge_dropouts]
+            wghts = batch[i][3][~edge_dropouts]
 
             # Clips node and edge solutions
-            nodesol = labels[i][0][:cropNodesTo]
-            edgesol = labels[i][1][:last_node_idx]
+            nodesol = labels[i][0][:cropTo]
+            edgesol = labels[i][1][~edge_dropouts]
             globsol = labels[i][2].astype(np.float)
 
             inputs[0].append(nodef)