As noted by @egreg, the parentheses in the math font for charter used by mathdesign appear to be the issue. Interestingly, the utopia font option in mathdesign behaves similarly.
\documentclass[10pt]{article}
\usepackage[utopia]{mathdesign}
\usepackage[T1]{fontenc}
\begin{document}
The mass as a function of time ($M(t)$).
\end{document}
yields:

I corrected the problem for Bitstream-Charter by replacing the delimiters with the appropriate characters in the mdbch font.
\documentclass[10pt]{article}
\usepackage[T1]{fontenc}
\usepackage[bitstream-charter]{mathdesign}
\AtBeginDocument{%
\DeclareSymbolFont{bch}{T1}{\rmdefault}{m}{n}%
\DeclareMathDelimiter{(}{\mathopen}{bch}{'050}{largesymbols}{"00}%
\DeclareMathDelimiter{)}{\mathopen}{bch}{'051}{largesymbols}{"01}%
}
\begin{document}
The mass as a function of time ($M(t)$).
\end{document}

XCharterbut it doesn't seem much different, even with the scaling option recommended in the documentation.mathdesignmath font for Charter are apparently badly designed.:-(