The check for when a node is a coordinate doesn't add the prefix/suffix in use and so fails if the name prefix or name suffix key has been used (that is, a node defined as a coordinate is not recognised as such).
The issue is in \tikz@parse@node and the following is a proposal for a fix.
\def\tikz@parse@node#1(#2){%
\pgfutil@in@.{#2}% Ok, flag this
\ifpgfutil@in@
\tikz@calc@anchor#2\tikz@stop%
\else%
\tikz@calc@anchor#2.center\tikz@stop% to be on the save side, in
% case iftikz@shapeborder is ignored...
% The next line is the fixed line with the addition of the `\tikz@pp@name`
\expandafter\ifx\csname pgf@sh@ns@\tikz@pp@name{#2}\endcsname\tikz@coordinate@text%
\else
\tikz@shapebordertrue%
\def\tikz@shapeborder@name{\tikz@pp@name{#2}}%
\fi%
\fi%
\edef\tikz@marshal{\noexpand#1{\noexpand\pgfqpoint{\the\pgf@x}{\the\pgf@y}}}%
\tikz@marshal%
}
See http://tex.stackexchange.com/q/327007/86 for a question on TeX-SX pertaining to this.
Thank you for reporting. The provided patch at the TeX.SX answer is incorporated now.