I dunno about modern altium, but older versions had the option for the footprint of a components which set if you wanted to use a specific footprint in a specific library, or use any footprint in any installed library with the correct name. If you had it set the latter and used a common name I can see it getting confused and picking something other than what you had intended.
Also FYI, if you update SCH to PCB and then notice your PCB is all messed up you can always just undo that change like you would undo anything. The PCB update is part of undo history. Obviously you need enough undo-history to get back to the change if you didnt notice right away.
I use that from time to time, Update SCH to PCB, ops that's wrong, CTRL-Z