diff --git a/coverage-tool/coverage-reporting/clone_sources.py b/coverage-tool/coverage-reporting/clone_sources.py
index ec38acd..99c80ab 100644
--- a/coverage-tool/coverage-reporting/clone_sources.py
+++ b/coverage-tool/coverage-reporting/clone_sources.py
@@ -71,6 +71,7 @@
                     print(("WARNING!: Mismatch in git repo {}\nExpected {}, "
                            "Cloned {}").format(source['URL'], source['COMMIT'],
                                                commit_id))
+                    return True
         elif source['type'] == "http":
             if handler is not None:
                 return handler(source,
@@ -124,7 +125,7 @@
                 url = git["URL"]
                 commit_id = git["COMMIT"]
                 output_loc = os.path.join(output_dir, git["LOCATION"])
-                cmd = "git clone {} {}".format(url, output_loc)
+                cmd = "rm -rf {1} || true;git clone {0} {1}".format(url, output_loc)
                 output = call_cmd(cmd)
                 if git['REFSPEC']:
                     call_cmd("cd {};git fetch -q origin {}".format(
diff --git a/coverage-tool/coverage-reporting/merge.sh b/coverage-tool/coverage-reporting/merge.sh
index 635b1f2..899a784 100755
--- a/coverage-tool/coverage-reporting/merge.sh
+++ b/coverage-tool/coverage-reporting/merge.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 ##############################################################################
-# Copyright (c) 2020, ARM Limited and Contributors. All rights reserved.
+# Copyright (c) 2020-2025, ARM Limited and Contributors. All rights reserved.
 #
 # SPDX-License-Identifier: GPL-2.0-only
 ##############################################################################
@@ -374,6 +374,8 @@
   echo "[-m <JSON filename>]  JSON merged SCM sources. Defaults to ./merged_scm.json"
   echo "[-c]                  Flag to download/copy the source files from the JSON merged SCM into the workspace directory."
   echo "[-g]                  Flag to generate local reports for each info/json instance."
+  echo "[-i]                  Ignore errors on genhtml."
+  echo "[-d]                  Enable debug mode for the script."
   echo "$help_message"
 }
 
@@ -393,7 +395,12 @@
 info_files=() # Array of info files
 json_files=() # Array of configuration json files
 list_of_merged_builds=()
-while getopts ":hj:o:l:w:i:cm:g" opt; do
+GENHTML_ARGS=""
+DEBUG_MODE=false
+genhtml_version=$(genhtml --version | rev | cut -d ' ' -f1 | rev | xargs)
+gen_major=$(echo "$genhtml_version" | cut -d '.' -f1)
+gen_minor=$(echo "$genhtml_version" | rev | cut -d '.' -f1 | rev)
+while getopts ":hj:o:l:w:idcm:g" opt; do
   case ${opt} in
     h )
       usage
@@ -405,6 +412,12 @@
     c )
       CLONE_SOURCES=true
       ;;
+    d )
+      DEBUG_MODE=true
+      ;;
+    i )
+      GENHTML_ARGS="${GENHTML_ARGS} --ignore-errors $([ $gen_major = '2' ] && echo inconsistent || echo source)"
+      ;;
     j )
       merge_configuration_file=$OPTARG
       ;;
@@ -435,6 +448,7 @@
       ;;
   esac
 done
+[ $DEBUG_MODE = true ] && set -x || set +x
 shift $((OPTIND -1))
 if [ -z "$merge_configuration_file" ]; then
   echo "Merged configuration file required."
@@ -452,7 +466,9 @@
 merged_coverage_file="$(get_abs_path $merged_coverage_file)"
 merged_json_file="$(get_abs_path $merged_json_file)"
 param_cloned=""
-get_info_json_files
+set +x
+get_info_json_files # always disabled for debug
+[ $DEBUG_MODE = true ] && set -x || set +x
 merge_files
 if [ $CLONE_SOURCES = true ];then
     clone_repos $merged_json_file
@@ -460,7 +476,7 @@
 
 # Generate merged coverage report
 merged_status=true
-genhtml --branch-coverage $merged_coverage_file \
+genhtml $GENHTML_ARGS --branch-coverage $merged_coverage_file \
     --output-directory $LCOV_FOLDER
 if [ $? -ne 0 ];then
     merged_status=false