I don't remember exactly (my autoconf/automake-fu has gotten weak these past years), but there's a macro AM_MAINTAINER_MODE that will add --enable/disable-maintainer-mode as an option to your configure script that will determine if rules get added to the final Makefile that will check to see if Makefile.am is newer than Makefile.in or if Makefile.in is newer than Makefile, or if configure.ac is newer than configure (etc.) and then attempt to regenerate them.

I don't quite remember what the default is if you don't include AM_MAINTAINER_MODE in your configure.ac. So yes, you could have indeed seen that happen, but there are ways to make it not happen.