Yes this can definitely be the case. I had a Y sector on SQ last month on an AirNZ ticket. I used some UA points to upgrade the sector and this put my UA ff number into the sector without my knowing and possibly the rest of the booking.. Luckily the SQ check in agent politely told me he couldn’t see my Star Alliance gold status which alerted me to what had happened. I needed those status points from the flight to accrue to my AirNZ ff account so that was lucky.