diff --git a/pdgstaging/ConfigManager.py b/pdgstaging/ConfigManager.py
index 81e4ef8..8800c94 100644
--- a/pdgstaging/ConfigManager.py
+++ b/pdgstaging/ConfigManager.py
@@ -1265,7 +1265,7 @@ def get_deduplication_config(self, gdf=None):
 
             for f in files:
                 try:
-                    footprints[f] = self.footprint_path_from_input(f)
+                    footprints[f] = self.footprint_path_from_input(f, check_exists=True)
                 except FileNotFoundError:
                     logger.warning(
                         f'No footprint files found for file {f}. '
@@ -1349,10 +1349,10 @@ def footprint_path_from_input(self, path, check_exists=False):
         path = os.path.join(dir_footprints, path + ext_footprints)
         if check_exists:
             if os.path.exists(path):
-                logger.info('Successfully found footprint file: {}'.format(path))
+                logger.info(f'Successfully found footprint file: {path}')
                 return path
             else:
-                logger.info('Failed to find footprint file: {}'.format(path))
+                logger.info(f'Failed to find footprint file: {path}')
                 raise FileNotFoundError(path)
         else:
             return path
diff --git a/pdgstaging/Deduplicator.py b/pdgstaging/Deduplicator.py
index 0e53794..4145a38 100644
--- a/pdgstaging/Deduplicator.py
+++ b/pdgstaging/Deduplicator.py
@@ -521,7 +521,11 @@ def deduplicate_by_footprint(
     # paths and load the footprints
     if all([isinstance(v, str) for v in footprints.values()]):
         for name, path in footprints.items():
-            footprints[name] = gpd.read_file(path)
+            try:
+                footprints[name] = gpd.read_file(path)
+            except Exception:
+                footprints[name] = None
+                warnings.warn(f'Footprint missing for {name}')
 
     # Add a column to the GeoDataFrame that contains the filename
     prop_filename_temp = 'filename_' + uuid.uuid4().hex
@@ -534,9 +538,12 @@ def deduplicate_by_footprint(
     # Clip to gdf to the extent of the footprints
     if clip_to_footprint:
         for name, gdf_grp in gdf_dict.items():
+            fp = footprints.get(name)
+            if fp is None:
+                continue
             clip_results = clip_gdf(
                 gdf=gdf_grp.copy(),
-                boundary=footprints[name].copy(),
+                boundary=fp.copy(),
                 method=clip_method)
             gdf_dict[name] = clip_results['keep']
             removed.append(clip_results['removed'])
@@ -557,8 +564,10 @@ def deduplicate_by_footprint(
     for pair in itertools.combinations(names, 2):
         name1 = pair[0]
         name2 = pair[1]
-        footprint1 = footprints[name1]
-        footprint2 = footprints[name2]
+        footprint1 = footprints.get(name1)
+        footprint2 = footprints.get(name2)
+        if(footprint1 is None or footprint2 is None):
+            continue
 
         # Get overlap between two footprints
         overlap = gpd.GeoDataFrame(
@@ -587,7 +596,7 @@ def deduplicate_by_footprint(
         removed.append(to_reduce[overlap_boolean])
 
     # Recombine the GDFs from the dictionary
-    keep = pd.concat(gdf_dict.values())
+    keep = pd.concat(gdf_dict.values(), ignore_index=True)
     removed = pd.concat(removed)
 
     to_return = {
@@ -596,7 +605,7 @@ def deduplicate_by_footprint(
     }
 
     if return_intersections:
-        to_return['intersections'] = pd.concat(intersections)
+        to_return['intersections'] = pd.concat(intersections, ignore_index=True)
 
     if label:
         to_return = label_duplicates(to_return, prop_duplicated)
diff --git a/pdgstaging/TileStager.py b/pdgstaging/TileStager.py
index 06a358c..a14f676 100644
--- a/pdgstaging/TileStager.py
+++ b/pdgstaging/TileStager.py
@@ -466,7 +466,7 @@ def combine_and_deduplicate(self, gdf, tile_path):
         if num_unique_crs != 1:
             existing_gdf.to_crs(gdf.crs, inplace=True)
 
-        gdf = pd.concat(to_concat)
+        gdf = pd.concat(to_concat, ignore_index=True)
         dedup_config = self.config.get_deduplication_config(gdf)
         if dedup_method is None:
             return gdf
diff --git a/setup.py b/setup.py
index c34caf0..8a53d96 100644
--- a/setup.py
+++ b/setup.py
@@ -16,8 +16,8 @@
     install_requires=[
         'numpy >= 1.2, < 2.0',
         'pandas >= 1.4, < 2.0',
-        'shapely >= 2.0b2',
-        'geopandas >= 0.12, < 1.0',
+        'shapely >= 2, < 3.0',
+        'geopandas >= 0.12.2, < 1.0',
         'morecantile >= 3.1, < 4.0',
         'Rtree >= 0.9, < 1.0',
         'filelock >= 3.6, < 4.0',