What is the one problem for the male and female reproductive system?

I am not sure what you are asking here or if you are
talking about plant or animals.

 For plants if there are
both male and female plants and they are on separate plants the problem that might occur
is how the gametes can get together - in other words how will pollination occur.  The
plant world has solved this in many ways such as air pollination, insect pollination
etc.

For some animals such as those that are not very
mobile this problem is similar.  For most animals the issue is not finding each other
but the timing and making sure that they are breeding with the correct species.  Animals
have worked this out through things such as mating displays, pheremones, and timing the
reproductive cycles.