diff --git a/src/pynxtools/testing/nexus_conversion.py b/src/pynxtools/testing/nexus_conversion.py
index 3fc02c721..7eed6a027 100644
--- a/src/pynxtools/testing/nexus_conversion.py
+++ b/src/pynxtools/testing/nexus_conversion.py
@@ -43,6 +43,7 @@ def get_log_file(nxs_file, log_file, tmp_path):
     logger = logging.getLogger("pynxtools")
     logger.handlers.clear()
     logger.setLevel(logging.DEBUG)
+    logger.propagate = False
     log_file = os.path.join(tmp_path, log_file)
     handler = logging.FileHandler(log_file, "w")
     formatter = logging.Formatter("%(levelname)s - %(message)s")
@@ -195,10 +196,24 @@ def check_reproducibility_of_nexus(self, **kwargs):
 
         SECTION_SEPARATOR = "DEBUG - ===== "
 
-        def should_skip_line(gen_l: str, ref_l: str, ignore_lines: list[str]) -> bool:
-            """Check if both lines start with any ignored prefix."""
+        def should_skip_line(*lines: str, ignore_lines: list[str]) -> bool:
+            """
+            Check if all given lines start with any ignored prefix.
+
+            Parameters
+            ----------
+            *lines : str
+                One or more lines to check.
+            ignore_lines : list[str]
+                List of prefixes to ignore.
+
+            Returns
+            -------
+            bool
+                True if all lines start with any of the ignored prefixes.
+            """
             return any(
-                gen_l.startswith(ignore) and ref_l.startswith(ignore)
+                all(line.startswith(ignore) for line in lines)
                 for ignore in ignore_lines
             )
 
@@ -214,35 +229,63 @@ def load_logs(
 
         def compare_logs(gen_lines: list[str], ref_lines: list[str]) -> None:
             """Compare log lines, ignoring specific differences."""
+
+            def extra_lines(
+                lines1: list[str], lines2: list[str]
+            ) -> list[Optional[str]]:
+                """Return lines in lines1 but not in lines2, with line numbers and ignoring specified lines."""
+                diffs: list[Optional[str]] = []
+                section_ignore_lines = []
+                section = None
+                for ind, line in enumerate(lines1):
+                    if line.startswith(SECTION_SEPARATOR):
+                        section = line.rsplit(SECTION_SEPARATOR)[-1].strip()
+                        section_ignore_lines = IGNORE_SECTIONS.get(section, [])
+                    if line not in lines2 and not should_skip_line(
+                        line, ignore_lines=IGNORE_LINES + section_ignore_lines
+                    ):
+                        diffs.append(f"{line.strip()} (line: {ind})")
+                return diffs
+
+            # Case 1: line counts differ
             if len(gen_lines) != len(ref_lines):
-                raise AssertionError(
+                diffs_gen = extra_lines(gen_lines, ref_lines)
+                diffs_ref = extra_lines(ref_lines, gen_lines)
+
+                error_msg = (
                     f"Log files are different: mismatched line counts. "
                     f"Generated file has {len(gen_lines)} lines, "
                     f"while reference file has {len(ref_lines)} lines."
                 )
-
+                if diffs_gen:
+                    error_msg += "\n\nExtra lines in generated:\n" + "\n".join(
+                        diffs_gen
+                    )
+                if diffs_ref:
+                    error_msg += "\n\nExtra lines in reference:\n" + "\n".join(
+                        diffs_ref
+                    )
+
+                raise AssertionError(error_msg)
+
+            # Case 2: same line counts, check for diffs
+            diffs = []
             section_ignore_lines = []
             section = None
-
-            diffs = []
             for ind, (gen_l, ref_l) in enumerate(zip(gen_lines, ref_lines)):
                 if gen_l.startswith(SECTION_SEPARATOR) and ref_l.startswith(
                     SECTION_SEPARATOR
                 ):
                     section = gen_l.rsplit(SECTION_SEPARATOR)[-1].strip()
                     section_ignore_lines = IGNORE_SECTIONS.get(section, [])
-
-                # Compare lines if not in ignore list
                 if gen_l != ref_l and not should_skip_line(
-                    gen_l, ref_l, IGNORE_LINES + section_ignore_lines
+                    gen_l, ref_l, ignore_lines=IGNORE_LINES + section_ignore_lines
                 ):
-                    diffs += [
-                        f"Log files are different at line {ind}\ngenerated: {gen_l}\nreferenced: {ref_l}"
-                    ]
-
+                    diffs.append(
+                        f"Log files are different at line {ind}:\n  generated: {gen_l}\n  reference: {ref_l}"
+                    )
             if diffs:
-                diff_report = "\n".join(diffs)
-                raise AssertionError(diff_report)
+                raise AssertionError("\n".join(diffs))
 
         # Load log paths
         ref_log_path = get_log_file(self.ref_nexus_file, "ref_nexus.log", self.tmp_path)