The title by itself is intriguing but gives little clue to the content.
The first stanza seems to suggest that you question 'heaven' and therefore religion, that the wishing well is merely a hole in the ground, a source of water but not for wishes. The tone of the poem is set here, you liken heaven with wishes and doubt both.
The theme continues in the second stanza. You've chased the end of the rainbow, finding no pot of gold, only dirt and lost dreams, 'haunting' your poems, you're disillusioned.
In the third stanza, you describe how awful it would be if nature also didn't behave as expected (like religion?) the cuckoo leaves the nest during autumn rather than spring, and a bee without the very sting that makes it a bee.
Your concluding stanza describes your confusion over whether you'll ever understand what it is that defines good and bad, when 'good' people do bad things. It's like thinking that the sunshine (good) is actually snow (bad). And now the title makes sense.
Beautifully written with impeccable rhyming and meter! :-) x