Yes, originally, the code stopped searching when it found the first reduction. Given the order in which these are searched, it didn't produce this garbage. I only changed this behavior before pasting the code, because it may be interesting to see multiple possibilities (like with E(21/32) = E(3/4) & E(7/8) = E(1/2) | E(5/16)), and I didn't notice the noise.

To fix it, change
if ($denominator2 > $numerator2) {
to
if ($denominator1 > $numerator1 && $denominator2 > $numerator2) {
but I'm sure you know that.