Underfull \vbox (badness 10000) has occurred while \output is active

You have specified a page size and removed any stretch space between paragraphs, so if you have a page of text that has no display material there is no way for tex to fill the page unless the textheight is an exact multiple of baselineskip, plus the 1em for each paragraph separation.

Perhaps you want \raggedbottom to allow (every) page to be short, it is hard to tell just from teh fragments that you have shown.

You have to announce \doublespacing before geometry sets up the page dimensions; you also should add heightrounded and give a little flexibility to \parskip.

\documentclass{book}

\usepackage{geometry}
\usepackage{fancyhdr}
\usepackage{setspace} %for doublespacing

\doublespacing %double spacing
\geometry{
  a4paper,
  left=1.5in,
  right=1.5in,
  top=1in,
  bottom=1in,
  heightrounded,
}


\setlength{\parindent}{4em} %spacing of beginning of a new paragraph
\setlength{\parskip}{1em plus 0.1em}   %spacing between paragraphs
%\renewcommand{\cleardoublepage}{\clearpage} %for the headings

\usepackage{lipsum}

\begin{document}

\lipsum[1-30]

\end{document}

But do you really want a large parindent, a non zero parskip along with double spacing? The end result is horrible!