Edit 2023-03-28
A firstaid for cleveref has been added to LaTeX which contains the redefinitions mentioned in the answer. With the next LaTeX release and with the latex-dev released today the references will be correct again.
Old Answer
In a current LaTeX, the syntax of \newlabel in the .aux file has been unified with the syntax used by hyperref and always contains five data containers. cleveref has not been adapted to this change and still only uses two data container in its definition. So your external .aux file contains (I added some spaces for better visibility):
\newlabel{sec:one}{ {1} {1} {One} {section.1} {} } %<------- five
\newlabel{sec:one@cref}{ {[section][1][]1} {[1][1][]1} } %<------- two
Inside a document it doesn't matter so much that the cleveref label has only two data container, as cleveref is the only one using it. But xr-hyper tries to adhere to the new standard too and extends every label it reads to five data container. It also makes use of the fifth data container to store the file name for links.
Now, recently xr-hyper has been extended to store always the file name (and not only if the label contains a destination name in the fourth container) to allow file links to the external document even if that document didn't use hyperref. With this change one gets this definitions for the labels from the external document:
> \r@sec:one=macro:
->{1}{1}{One}{section.1}{fileone.pdf}.
> \r@sec:one@cref=macro:
->{[section][1][]1}{[1][1][]1}{}{}{fileone.pdf}.
% would be in older versions:
% ->{[section][1][]1}{[1][1][]1}{}{}{}.
And then cleveref falls over the fileone.pdf in the last argument.
The best would be if cleveref would be updated to use the standard five data container always too, so that everything is in sync. For now, you can do something like this:
\documentclass{article}
\usepackage{xr-hyper}
\usepackage{hyperref}
\usepackage{cleveref}
\externaldocument{fileone}
\makeatletter
\def\cref@getref#1#2{%
\expandafter\let\expandafter#2\csname r@#1@cref\endcsname%
\expandafter\expandafter\expandafter\def%
\expandafter\expandafter\expandafter#2%
\expandafter\expandafter\expandafter{%
\expandafter@firstoffive#2}}% <-------- five
\def\cpageref@getref#1#2{%
\expandafter\let\expandafter#2\csname r@#1@cref\endcsname%
\expandafter\expandafter\expandafter\def%
\expandafter\expandafter\expandafter#2%
\expandafter\expandafter\expandafter{%
\expandafter@secondoffive#2}}% <----------- five
\AtBeginDocument{%
\def\label@noarg#1{%
\cref@old@label{#1}%
@bsphack%
\edef@tempa{{page}{\the\c@page}}%
\setcounter{page}{1}%
\edef@tempb{\thepage}%
\expandafter\setcounter@tempa%
\cref@constructprefix{page}{\cref@result}%
\protected@write@auxout{}%
{\string\newlabel{#1@cref}{{\cref@currentlabel}%
{[@tempb][\arabic{page}][\cref@result]\thepage}{}{}{}}}% <----- five
@esphack}%
\def\label@optarg[#1]#2{%
\cref@old@label{#2}%
@bsphack%
\edef@tempa{{page}{\the\c@page}}%
\setcounter{page}{1}%
\edef@tempb{\thepage}%
\expandafter\setcounter@tempa%
\cref@constructprefix{page}{\cref@result}%
\protected@edef\cref@currentlabel{%
\expandafter\cref@override@label@type%
\cref@currentlabel@nil{#1}}%
\protected@write@auxout{}%
{\string\newlabel{#2@cref}{{\cref@currentlabel}%
{[@tempb][\arabic{page}][\cref@result]\thepage}{}{}{}}}% <------- five
@esphack}%
}
\begin{document}
\Cref{sec:one}
\end{document}