1) Sometimes a make complains that aclocal-<version> is missing. It is in fact present, but a different version. It's possible to clear this warning by doing a make distclean followed by ./configure and make. I'm not sure what triggers this; I suspect that the `missing` script doesn't get rebuilt when the tools it's checking get updated.
2) Sometimes the info top page (not the APL top, but the system top) gets corrupted and shows additional copies of the `APL` entry along with some "random" control and high-bit characters. I have no idea what triggers this. Here's an example from one of my installations. Note that the presentation may be a bit different from what I see in Emacs; GMail tries to make sense of the apparently-Unicode characters.
BTW, this seems to be an Emacs-only thing; running info in a terminal does not list an entry for APL in the top page.