You have given very few clues but I assume you have done this
\documentclass[twoside]{report}
\setlength\parskip{1em}
\begin{document}
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
one two three one two three one two three one two three one two three
\end{document}
which produces the warning
Underfull \vbox (badness 10000) has occurred while \output is active [1
The problem is that the document class has specified that the last line of each page should be at the bottom of the page, but you have removed all flexibility from \parskip and set it to a length which is not a multiple of \baselineskip.
The standard classes default the textheight to be \topskip plus a multiple of \baselineskip precisely to avoid this problem, so a page full of text fits the page exactly. But if you have a page with no stretchable space (so no headings or lists or equations that have stretch space around them) and you have set \parskip to a value that does not stretch, and is not a multiple of \baselineskip then the page inevitably ends short and there is no way to expand it to fill the specified space so it is underfull.
If instead of 1em you set
\setlength\parskip{\baselineskip}
or
\setlength\parskip{1em plus 2pt}
then the warning goes and the bottom line of text is at the bottom of the page.
\inputfiles by copying in the text of the file at that point, then delete all text before the page with the box then delete any packages not needed for the example, that makes an example anyone can run to see the problem. – David Carlisle May 27 '17 at 13:20\setlength{\parskip}{1em}that removes all flexibility, and adds a length which is not\baselineskipso any page that just has text and no displayed lists etc but has a paragraph break will necessarily make an underfull box. – David Carlisle May 27 '17 at 15:33