There are various reasons that can happen. For instance, at Pac-12 Champs, you are limited in the number of swimmers in an event that are allowed to score. (Not sure what that number is today - it used to be 3) So, you can have several swimmers in an event - but, that means you will have some swimmers compete "exhibition" - their times are legitimate (so they can qualify for NCAAs), but no matter how fast they swim, they cannot score for the university. However, this is not the case at NCAAs. So, the teams with more 'quality depth' are able to score more --> since any of their swimmers entered in the event are able to score points. (So, 'quality depth' is rewarded at NCAAs.)
Also, the swimmers that have already qualified for NCAAs (comfortably - not those on the bubble) usually aren't shaved and fully tapered at Pac-12s. Whereas, those swimmers (from any school) that are trying to qualify for NCAAs will be shaved and fully tapered at Pac-12s and might beat the un-tapered (but NCAA qualified) swimmers at Pac-12s. However, those same swimmers usually either just maintain their times (at best), or slightly add to their qualifying times at NCAAs because they're trying to extend their taper --> which can be really hard to do - the longer the event, the harder it is. [One of the tell-tale signs of that (especially in the longer events) is someone that swims well in the morning (during trials), but then adds to that time in finals.] Whereas, the swimmers that weren't shaved and fully tapered at Pac-12s WILL be shaved and fully tapered at NCAAs, and will have their best swims of the season at that meet. (and beat the people that beat them at Pac-12s)
Another example is that some swimmers that have already qualified for NCAAs in their 'main events' - might swim other, secondary, events at Pac-12s either to (a) try to qualify for NCAAs in another event at which they're very good, or to (b) take a break from their "typical events" and swim events that they enjoy. Also, some NCAA qualified swimmers prefer to not to swim their main events at a 'pre-championship meet' because it can hurt their confidence to swim their main events, untapered, and either (i) not swim as fast as they would like/expect to because they aren't shaved and tapered, and/or (ii) be beaten by other swimmers that are tapered - because they aren't tapered - as both of those scenarios can mess with your head a bit.
Those are a few examples
WAY TO GO CAL BEAR M.SWIMMERS!!!!
GO BEARS!!!!