This usually happens with the lighter weight papers such as 90 -140lb papers and especially if the paper was not stretched before painting. This is one reason why I like to use heavier weight papers for instance 300lb, this way I don't really have to worry about the problem.
All of us artist's would like to think that the viewer can see beyond the wobbly paper to the actual piece of art, that can be true, but that's not always the case. To show your work at it's best, before framing, consider flattening the painting first.
Option 1: All you have to do is place the painting face down on a clean towel then "lightly" spray the back with clean water, then place another flat surface on top of the painting (such as a piece of Plexiglas or foam core) then weight it down and let completely dry. Your environment will determine the drying time.
Option 2: A quicker way to do it, is to again place the painting face down on a clean towel then "lightly" spray the back of the painting with clean water, then using an iron on a "low heat" lightly iron the back to flatten.