If Species B did indeed “come from” Species A this in no way means that Species A can no longer exist.
If, for example, Species A exists over a range. If a population of Species A becomes geographically isolated (for any number of reasons) then that population can evolved independently of the rest. Given sufficient time, and sufficiently different evolutionary pressures, the isolated population could indeed evolve into a new species: Species B. Meanwhile, Species A could continue on its merry way. Boom - Species B “came from” Species A and yet they coexist.
