I never applied these payments against this invoice, any idea what has gone wrong?

Ok. There is zero logic or software to auto pay items.

Maybe you did it by accident when reconciling.

Yep. You can part pay bills etc.

If the invoice has a payment against it someone made that payment in Bullet. We've no software to do that at all we can't make those calls cause it impacts so much of the product.
If you've submitted that tax return then you should talk to your accountant. They might say to leave it. If not you'll need to resubmit a VAT adjustment and manually adjust Bullet - we've no work flows for that.
If you haven't submitted the vat return. Then click tax the vat return for that period. On the right click unpaid, delete the payment on the invoice and remark paid on the tax return.

The logs just tell you what you can see. That's all.

It's usually always human error Shane. But, nobody likes to hear that

Nope.

Sorry about that.