Just a guess here, as it's been a while since I've added a card to Wallet (and do not want to remove one just for testing purposes), but, depending on issuing bank, might not need much information off credit card to enter manually into Apple Pay on their device.
At that point, issuer might be doing standard security checks like what happened. Eg. real owner buys stuff generally in one city/state, and all of a sudden a charge going in across the country, especially if large? Especially easy to spot if card was used earlier in the day in home area.
Or, card was flagged if a bad guy was trying to guess, for example, the CVV code when trying to register. And when a possibly cloned card was attempted to be used, all sorts of flags go off (ie. a whole crew of thieves are using the CC skimmed off a standard swipe reader, for example).
Big issue: your Apple ID might be compromised. Go into appleid.apple.com and verify no strange devices are listed. And to be safe, change your password. This might be why you are seeing Apple Pay notifications.
ADD: in general, Apple Pay is secure. System is similar to the chip in credit cards. CC issuer generates a fake CC number that gets stored on the device in the Secure Enclave (no app/software access to that). Any CC transaction with Apple Pay sends the fake number with a random counter value, and if jives with what CC issuer has on file, they send back a one-time use CC number for the merchant to use. So if merchant's systems get hacked, the CC number they have for the charge for you cannot be used due to single use number (and that's maybe why the CC issuer flagged it: thieves hacked some merchant's system and tried to use the one-time use number and issuer knows it's a single-use number).