Having f--ked up a few things in my time (and don't tell me you've never done so at your job!) I can't rule out the possibility that this is what happened.
However, a couple things - first, they didn't removed the root; just the nerve inside. This is like saying if you have a clogged sink they remove the pipes. Well, no, root canal is exactly like a Roto-rooter, except you don't see the guys butt-crack. :)
Second - if you went to a specialist, they really know their stuff... i mean, he went to college and four years of dental school and THREE more years of root canal training.
That said, you could just have a REALLY tough tooth to work with.
you know which cardiac surgeons have the most patients die? The BEST ones...think about it...the one's w/ the worst chances are "passed" on by the normal surgeons... "Oh, this looks like a job for Dr. Smith!" and even the best docs can have stuff go south. They come out of the OR and say, "I'm sorry...we did everything we can, but....
Back to helping YOU. three ibuprofens a day is NOTHING! I wouldn't take more than four a day normally, but if you don't have GI/stomach issues, you can take up to 3-4 ibu every 4-6 hrs and be fine. If I were you, i'd start on 2 ev. 4 hrs and go from there...do this for a few days. you should call your endodontist, however, and let them know. You may need add'l antibiotic to clear up residual infection and you may even need a little vicodin or soemthing to get you over the hump.
Hope my explanation has helped. Honestly, tho', if you didn't understand all this before, it's kind of a shame - when I make my patients pay $1000 or whatever for some procedure, I make sur ethey know damned well what I'm doing, what can go wrong, and how to take care of themselves after. Also, they have my cell phone for emergencies.. So maybe find a dentist that does that, but your current ones may be fine.
good luck!