Fraudulent activity on checking account.

Not sure anyone here would know anything about this, but I guess it can't hurt to ask. A little background, I keep two checking accounts. One I use in the real world, day to day life and almost never online. The other one I only use online and I only keep enough money in the account to cover purchases I've made. About 3 weeks ago I received a charge to that checking account from afterpay that I knew I had not made. I have used afterpay a few times, although not for a couple years, but I do have an account with them so I downloaded their app and interestingly enough there was no activity on my account even though there was a charge for them on my checking account. Contested it with the bank, got my money back. Completely closed the account and open a new one.

Now to me here's where it gets kind of weird. I made a purchase from a company through PayPal for let's say $1,000. They sent an invoice to PayPal and I approved it and paid them. Now the owner of this company uses a completely different one to invoice. So looking at my PayPal account, at least for my side of the computer screen, would not lead back to the company I actually made the purchase from. Three days later I woke up to my account overdrawn and a withdrawal from PayPal for $999 with the name of the company that I had made the initial purchase from attached to it. Not the name of the company that was used to bill me. Called and spoke to the owner of the company and he assured me he had nothing to do with it, which I believe because it's a reputable company. Called PayPal and after an hour on the phone they could not find the charge on their system and had no idea what it was, at least that's what they told me. And like the first one there was no activity to my Paypal account when I checked online. Went to the bank and got it reversed next day because it was still pending I assume. So all is well that ends well I guess. But what still bothers me is how someone made a withdrawal from my checking account, a brand new checking account mind you, in the name of the original company, and a dollar off of the original amount. I've never been frauded this way before in my life and now twice within a month over two different checking accounts. Anyone have any thoughts?