A quick diff and script to resolve cakephp/cakephp#7626 until that PR can be merged. Save these files in your project root dir, make the .sh executable, and run it. Assumes CakePHP v3.1.3 is in use.

belongstomany-patch.sh

#!/usr/bin/env bash

#---------------------------------------------------------------------
usage ()
{
	cat <<EOT

${0##*/}
    Apply the belongstomany.patch file to your cakephp source in vendor/

Usage:
    bin/${0##*/} <table>

EOT

	exit 0
}
if [ "$1" = '-h' ]; then
	usage
fi

DIR="$( cd -P "$( dirname "$0" )"/.. >/dev/null 2>&1 && pwd )"


printf "\n## Applying patch.\n"
patch vendor/cakephp/cakephp/src/ORM/Association/BelongsToMany.php belongstomany.patch

printf "\n## To undo, run 'composer install' or reset your vendor/ dir"
printf "\n## or run this again and choose 'Y' when prompted to reverse.\n"

belongstomany.patch

--- vendor/cakephp/cakephp/src/ORM/Association/BelongsToMany.php	2015-10-30 10:01:28.000000000 -0500
+++ vendor/cakephp/cakephp/src/ORM/Association/BelongsToMany.php	2015-10-30 10:01:49.000000000 -0500
@@ -758,6 +758,7 @@

                 $associationConditions = $this->conditions();
                 if ($associationConditions) {
+                    $existing->contain($this->target()->alias());
                     $existing->andWhere($associationConditions);
                 }