Yes and No. Tom is right. Dis-simmiliar metals will cause corrosions. It's called a galvanic reaction. However if you go to a gutter supply shop and ask for "gutter nails" you will get galvanized screw shank nails. I bring this up because most gutters are aluminum. Now that I think about it, most gutter zip screws and many rivets are painted galvinized. So will you get some corrosion? Yes, over time, not immediately. Is it worth freaking out over now? Probably not, In My Opinion. In 20 years it will certainly be a cause of concern. Now if you had copper mixed with galvanized that'd be a reason to freak out immediately.
I'm not sure why you'd have one flashing with another type of roof. Maybe some pictures would help.