diff --git a/coverage-tool/coverage-reporting/clone_sources.py b/coverage-tool/coverage-reporting/clone_sources.py
index ec38acd4a4786fadc6fad91f34fb31a1067c9993..99c80abc86cc278f0ae2d9ab8ceb60b3656cb7b5 100644
--- a/coverage-tool/coverage-reporting/clone_sources.py
+++ b/coverage-tool/coverage-reporting/clone_sources.py
@@ -71,6 +71,7 @@ def skip_source(output_dir, source, handler=None):
                     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 @@ class CloneSources(object):
                 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 635b1f20a4c6f566858a95616bd7a0807f88e80b..1034b79612848171497db629a59c6f0db435baca 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
 ##############################################################################
@@ -365,6 +365,8 @@ help_message=$(cat <<EOF
 EOF
 )
   clear || true
+  echo "Receiving arguments:"
+  echo $@
   echo "Usage:"
   echo "merge -h              Display this help message."
   echo "-j <JSON filename>    JSON configuration file (info and intermediate json filenames to be merged)."
@@ -374,10 +376,11 @@ EOF
   echo "[-m <JSON filename>]  JSON merged SCM sources. Defaults to ./merged_scm.json"
   echo "[-c]                  Flag to download/copy the source files from the JSON merged SCM into the workspace directory."
   echo "[-g]                  Flag to generate local reports for each info/json instance."
+  echo "[-i]                  Ignore errors on genhtml."
+  echo "[-d]                  Enable debug mode for the script."
   echo "$help_message"
 }
 
-
 [ ${-/x} != ${-} ] && TRACING=true || TRACING=false
 LOCAL_WORKSPACE=""
 CLONE_SOURCES=false
@@ -393,7 +396,13 @@ variables_file="./variables.sh"
 info_files=() # Array of info files
 json_files=() # Array of configuration json files
 list_of_merged_builds=()
-while getopts ":hj:o:l:w:i:cm:g" opt; do
+GENHTML_ARGS=""
+DEBUG_MODE=false
+genhtml_version=$(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)
+unset OPTIND
+while getopts ":hj:o:l:w:idcm:g" opt; do
   case ${opt} in
     h )
       usage
@@ -405,6 +414,12 @@ while getopts ":hj:o:l:w:i:cm:g" opt; do
     c )
       CLONE_SOURCES=true
       ;;
+    d )
+      DEBUG_MODE=true
+      ;;
+    i )
+      GENHTML_ARGS="${GENHTML_ARGS} --ignore-errors $([ $gen_major = '2' ] && echo inconsistent || echo source)"
+      ;;
     j )
       merge_configuration_file=$OPTARG
       ;;
@@ -435,6 +450,7 @@ while getopts ":hj:o:l:w:i:cm:g" opt; do
       ;;
   esac
 done
+[ $DEBUG_MODE = true ] && set -x || set +x
 shift $((OPTIND -1))
 if [ -z "$merge_configuration_file" ]; then
   echo "Merged configuration file required."
@@ -447,12 +463,15 @@ if [ -z "$LOCAL_WORKSPACE" ] && [ $CLONE_SOURCES = true ]; then
 fi
 # Getting the script folder where other qa-tools script files must reside, i.e
 # merge.py, clone_sources.py
+mkdir -p "${LCOV_FOLDER}"
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 LCOV_FOLDER="$(get_abs_path $LCOV_FOLDER)"
 merged_coverage_file="$(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 +479,7 @@ fi
 
 # 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