Common Configure/Make invocation of host built binaries on build machine!

Much more often then not, I come across a project with the usual configure, then make etc and the following issue:

the configure knows that this is a cross-compiling toolchain and yet... STILL... in various location during the "make" process, the system will try and invoke some recently built binaries; of course, they do not work: they are have been built for a different host system running a different architecture!

So, am I missing a commonly used option to configure other than build/host/target? I do read the disable/enable,with/without sections of the configure, but it is still not always clear which one to use. Things like --disable-testing make sense.

Or, are these just people that have made the build system under the assumption that the programs are always executable by the build machine!?

@rjd324

IIRC some (big) progams use some sort of self made tools to generate sources/headers. It comes to mind UAE.
So if you build on crosscompiler it may build for the host machine and not for the "destination build machine" or wherever you run then.