I had inexpensive roofers replace shingles this week. No leaks yet but I have looked at several web sites and feel they did the flashing around chimney wrong. The metal they covered the step flashing with has a flare on top that flares out away from chimney instead of being imbedded into the grout. They say "oh that won't leak!" Some guy at work had recommended them because his dad had his roof done but now I find out they offer a 200 $ kick back for referals.
What should I do?

Don't sweat it.

An educated customer is the best customer.

A roofing outfit doesn't want to have negative comments about their work, I doubt they left something that will leak.

If you'd like, post a picture of the roofline/chimney flashing and we here might be able to give you some more ideas.

Does the top flashing flare out at the bottom, or at the top, like it would catch the rain?

If it is embeded at the top and out at out at the bottom, it is proably counter flashing and is covering the shingle flashing below it. That would be OK.

Roger