Summary and Info:
makepkg sets $startdir to $PWD without resolving symlinks.
$BUILDDIR is set to the canonical path without symlinks.
If $startdir contains symlinks, these two paths differ and makepkg erroneously appends $pkgbase to the BUILDDIR.
This is especially bad if the package contains a file with the same name as it results in an error:

==> Making package: foo 1-1 (2018-06-04 ...)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
mkdir: cannot create directory ‘/tmp/aurbuild/foo/foo’: Not a directory

==> ERROR: An unknown error has occurred. Exiting...

A possible fix would be to initialize $startdir with $(pwd -P) or add it to the canonicalize_path loop.

Steps to Reproduce:

$ mkdir -p /tmp/aurbuild/foo
$ cd /tmp/aurbuild/
$ ln -s foo link
$ touch foo/foo
$ cat >foo/PKGBUILD <<PKGBUILD-end
pkgname=foo
pkgver=1
pkgrel=1
src=(foo)
md5sum=(SKIP)
arch=(any)
build() { false; }
package() { false; }
PKGBUILD-end
$ cd link
$ makepkg