This is a skill point.
To defeat the Queen using the wrench, simply do a 1-2-3 wrench attack. Approach the Queen from her side before hitting her with your wrench, or she will hit you with a reflex attack making this a lot harder. Hit her a few times, and she will turn to face you. When she is turning run to the opposite side of her and hit her again. Repeat this process as necessary.
When she sends out the frogs, hit them with a normal wrench attack. Eventually two larger lizards will attack you. Simply jump and press to do an overhead smash, as two of these will kill each of them.