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Your file[-3:] == ".py" check is later that it should be. It is part of the check executed for every line of a file, instead of only being done once per file. You should use:

for file in os.listdir(working_directory):
    if file[-3:] != ".py":
        ...

Are there other files in the directory? Maybe a README, Makefile.mak or .gitignore? Maybe you want to only examine .h files, and/or .hpp files, instead of every file in the directory?

valid_exts = { ".h", ".hpp"}
for file in os.listdir(working_directory):
    if os.path.splitext(file)[1] in valid_exts:
        ...

Using {line_number + 1} in your format string is not very pretty. Line numbers start at one, and enumerate() allows you to specify the starting number:

        for line_number, line in enumerate(source_file, 1):

Why accumulate the results in occurrences, and then write them out afterwords? Why not write them out as they are found?

with open("logs/log.txt", "w"):
    for file in os.listdir(working_directory):
        ...