So...as someone who owns like five SEs, some nickels of wisdom...
This being a used guitar...there is always a good chance the previous owner didn't do proper fretboard conditioning. Frets pop out sometimes if the board gets crazy dry, and can even sprout out of the sides. Thats not really a fault of the builders, I would blame the prior owner.
That said, I have seen new ones with frets that have lifted, but it's VERY few and far between. At the end of the day, the SE is easily one of the best (maybe the best) import guitars, period. Im sorry this was your first taste of the SE line, but I can assure you they are amazing guitars for the price. Do bear in mind, any guitar will need to be setup to your taste, and SEs do take a little extra work to optimize them, but its so with it. I do my own mods and fretwork on them so I just spend my time, but I would pit my SEs against American ones any day. They play better than most $3000 Les Pauls I've had the unfortunate pleasure of dealing with. Stick with it and I think you'll come to enjoy your SE.
Btw, if you keep your custom 24 and plan to use it for years to come, two big upgrades I recommend: replacing the saddles with mannmade machined ones and replace the nut. Those will be about $100 worth of upgrades, but I swear it's worth it.