incorrect output using re.sub()

You can use positivie lookahead assertion, which does not consume the matched part:

>>> re.sub(r"\.(?=[a-zA-Z])", ". ", string)
'This   is  very funny  and    cool. Indeed!'

Alternative using capturing group and backreference:

>>> re.sub(r"\.([a-zA-Z])", r". \1", string)  # NOTE - r"raw string literal"
'This   is  very funny  and    cool. Indeed!'

FYI, you can use \S instead of [a-zA-Z] to match non-space characters.

You could also use both lookahead and lookbehind in your regex.

>>> import re
>>> string="This   is  very funny  and    cool.Indeed!"
>>> re.sub(r'(?<=\.)(?=[A-Za-z])', r' ', string)
'This   is  very funny  and    cool. Indeed!'

OR

You may use \b,

>>> re.sub(r'(?<=\.)\b(?=[A-Za-z])', r' ', string)
'This   is  very funny  and    cool. Indeed!'

Explanation:

• (?<=\.) Just look after to a literal dot.
• (?=[A-Za-z]) Asserts that the matched boundary must be followed by a letter.
• If yes, then replace the boundary with space.