.Net regex matching $ with the end of the string and not of line, even with multiline enabled

It is clear your text contains a linebreak other than LF. In .NET regex, a dot matches any char but LF (a newline char, \n).

See Multiline Mode MSDN regex reference

By default, $ matches only the end of the input string. If you specify the RegexOptions.Multiline option, it matches either the newline character (\n) or the end of the input string. It does not, however, match the carriage return/line feed character combination. To successfully match them, use the subexpression \r?$ instead of just $.

So, use

@"^(#+).+?\r?$"

The .+?\r?$ will match lazily any one or more chars other than LF up to the first CR (that is optional) right before a newline.

Or just use a negated character class:

@"^(#+)[^\r\n]+"

The [^\r\n]+ will match one or more chars other than CR/LF.