diff --git a/pynestml/codegeneration/nest_code_generator.py b/pynestml/codegeneration/nest_code_generator.py
index 3045e03d5..66e0c9e13 100644
--- a/pynestml/codegeneration/nest_code_generator.py
+++ b/pynestml/codegeneration/nest_code_generator.py
@@ -177,7 +177,11 @@ def run_nest_target_specific_cocos(self, neurons: Sequence[ASTModel], synapses:
             # Check if the random number functions are used in the right blocks
             CoCosManager.check_co_co_nest_random_functions_legally_used(model)
 
-            if self.get_option("neuron_synapse_pairs"):
+            if Logger.has_errors(model):
+                raise Exception("Error(s) occurred during code generation")
+
+        if self.get_option("neuron_synapse_pairs"):
+            for model in synapses:
                 synapse_name_stripped = removesuffix(removesuffix(model.name.split("_with_")[0], "_"),
                                                      FrontendConfiguration.suffix)
                 # special case for NEST delay variable (state or parameter)
@@ -192,8 +196,8 @@ def run_nest_target_specific_cocos(self, neurons: Sequence[ASTModel], synapses:
                     delay_variable = self.get_option("delay_variable")[synapse_name_stripped]
                     CoCoNESTSynapseDelayNotAssignedTo.check_co_co(delay_variable, model)
 
-            if Logger.has_errors(model):
-                raise Exception("Error(s) occurred during code generation")
+                if Logger.has_errors(model):
+                    raise Exception("Error(s) occurred during code generation")
 
     def setup_printers(self):
         self._constant_printer = ConstantPrinter()
diff --git a/pynestml/frontend/pynestml_frontend.py b/pynestml/frontend/pynestml_frontend.py
index c257822de..59b9bb5f8 100644
--- a/pynestml/frontend/pynestml_frontend.py
+++ b/pynestml/frontend/pynestml_frontend.py
@@ -464,19 +464,22 @@ def process():
         Flag indicating whether errors occurred during processing
     """
 
-    # initialize and set options for transformers, code generator and builder
-    codegen_and_builder_opts = FrontendConfiguration.get_codegen_opts()
-
-    transformers, codegen_and_builder_opts = transformers_from_target_name(FrontendConfiguration.get_target_platform(),
-                                                                           options=codegen_and_builder_opts)
+    # initialise model transformers
+    transformers, unused_opts_transformer = transformers_from_target_name(FrontendConfiguration.get_target_platform(),
+                                                                          options=FrontendConfiguration.get_codegen_opts())
 
+    # initialise code generator
     code_generator = code_generator_from_target_name(FrontendConfiguration.get_target_platform())
-    codegen_and_builder_opts = code_generator.set_options(codegen_and_builder_opts)
+    unused_opts_codegen = code_generator.set_options(FrontendConfiguration.get_codegen_opts())
 
-    _builder, codegen_and_builder_opts = builder_from_target_name(FrontendConfiguration.get_target_platform(), options=codegen_and_builder_opts)
+    # initialise builder
+    _builder, unused_opts_builder = builder_from_target_name(FrontendConfiguration.get_target_platform(),
+                                                             options=FrontendConfiguration.get_codegen_opts())
 
-    if len(codegen_and_builder_opts) > 0:
-        raise CodeGeneratorOptionsException("The code generator option(s) \"" + ", ".join(codegen_and_builder_opts.keys()) + "\" do not exist.")
+    # check for unused codegen options
+    for opt_key in FrontendConfiguration.get_codegen_opts().keys():
+        if opt_key in unused_opts_transformer.keys() and opt_key in unused_opts_codegen.keys() and opt_key in unused_opts_builder.keys():
+            raise CodeGeneratorOptionsException("The code generator option \"" + opt_key + "\" does not exist.")
 
     models, errors_occurred = get_parsed_models()