From what I understand some of the original WA bugs seem to have come back with the University expansion and corresponding patch. I hope it's fixed quickly - my game used to suffer from them terribly. I've seen anecdotes of the same missing sim/other issues happening when sims go to University, so I'd caution everyone who sends a sim out of town to be extra careful!
What I used to do was always save before calling for a vacation. Most of the time the sims showed up in the destination, but if they didn't I'd quit without saving, re-launch Sims 3, re-load the save, and try sending them again. I never had an issue with the missing sims twice in a row.
However, if you start getting missing sims at home after travelling, that's a different bug altogether. My families used to bug out after another household member was added (mainly babies), and the worst part is it could happen days or weeks after the trip. Sims pictures would start vanishing from the side panel, they couldn't be controlled, they'd disappear from the lot, and eventually the file would be too corrupted to save, load, or play. I had a workaround if it was caught early enough (move the family to an empty lot, save the house to the library, save the family to the library, delete the current house and family, replace them both from the bin in their original lot). If I tried that too late, though, it didn't work.
My best advice is to have rotating saves (save1, save2, save3, etc), save both before travelling and before coming home, make sure you don't save over your departure or return save until you're sure everything is working fine, and until another patch is introduced to bear in mind that sims who travel might pick up some bugs along the way.