Little things like no upgrades (SFO-TPE-BKK is Thai operated code-share with a UA flight number from TPE-BKK. Hand in a Systemwide at SFO and it doesn't affect TPE-BKK).
Can't redeem awards on the code share flight.
There really is a whole list of things. The bottom line is that, if it has a UA flight number on it, it should be treated as a UA flight for ALL purposes. It surely isn't.