How did I end up with a version of Windows that wasn't genuine?

Four possibilities

(1) you installed a pirate copy of Windows - you know if you did this so there is no further explanation required here

(2) you bought a used computer that came with a pirate copy that you didn't know about - not anything you can do if you bought the computer from a person. Of course you could try to get your money back, but doubtful you will. If you bought it from a store/shop, then take it back. Hence, short of getting your money back on the purchase all you can do is buy a legal copy of WIndows

(3) you took your computer in for repair and they reinstalled Windows, but with a pirate copy - take the computer back and get your money back. If they refuse, you can take your issue to small claims court. You should also report it to Microsoft as they have a link for reporting shops that are pushing out stolen copies of WIndows to consumers

(4) you actually have a legal copy and are experiencing the false-positive software bug - this is a software bug in windows that has been around since Windows Vista. This happens to users who don't install their windows updates. Along the way all of a sudden the computer starts getting the "windows is not genuine" message, when in fact it's really a legal copy. That's why it's called the "false positive" software bug. This is easily fixed. All you have to do is install your windows updates. If this is the case with you, then you are way way WAY behind in windows updates because this bug is from years ago.

It's not always bootleg malware or virus may have erased your activation key.

Virus scan it and run malware bytes then run Windows activation use the activate by phone method in 80 percent of the cases smartphone method works

You didn't buy a genuine version.