Bitcoin Core uses a "keypool". When it first runs, it generates a list of 100 new addresses. After that, each time the user asks to "generate a new address" (or an address is needed for change, etc), the next address from the keypool list is used, and a freshly generated address is added to the end of the list to replace it. The keypool keys are stored in
wallet.dat along with your other private keys.
The purpose of this feature is so that when you back up
wallet.dat, you get not only the keys you have already used, but also the next 100 you will use. If this were not the case, then everytime you generated an address or made a transaction (generating a change address), you would have to immediately backup
wallet.dat again, and you'd be vulnerable to losing coins if your disk crashed in the meantime.
So when you copied the entire Bitcoin data directory, including wallet.dat, you also copied the keypool. As such, the next 100 addresses "generated" by both installations will be the same. After that they will differ.
But you probably didn't really want to share the wallet between both installations, since this can cause confusion unless you really pay attention to what you are doing. So you can delete the
wallet.dat from one of the installations (if you have made real transactions with it, back it up first) and let it be regenerated.