If your car already has issues (even if you haven't noticed them) then a remap will not necessarily cause any problems but will definitely exaggerate them to the point where you will notice them.
Any reputable tuning company will always run a pre-map health check ensuring there are no major issues.
I owned an Audi a2 a while back. Bought as a cheap run around - 200k on the clock, no service history, 5 previous owners and I think it was originally used as a rental car. Anyway I had it remapped to 100 from 75 bhp and pushed the torque up to 195 lbs/ft. Had absolutely no issues what so ever, no clutch slip or engine issues. I gave the car hell, and it took it quite happily.
Fast forward to 2014 - bought an s3 8l which had considerably less owners, full history etc... Got it remapped from 210 to 240 (so not even pushing it) and it exposed a world of issues! Leaks all over the place and general poor performance. All issues fixed now and touchwood it's running great albeit that it cost me a hell of a lot to put it right.
Bottom line, there is an element of luck involved. But getting the right map/tuner for your car is a good start, doesn't necessarily mean it will be plain sailing though.
