[jsmith613]

http://www.chemguide.co.uk/analysis/masspec/elements.html

If we look at the explanation for Chlorine we see that they say
" When chlorine is passed into the ionisation chamber, an electron is knocked off the molecule to give a molecular ion, Cl2+. These ions won't be particularly stable, and some will fall apart to give a chlorine atom and a Cl+ ion"

Why will only some fall apart and not all of it?

[Trave11er]

I guess, because this is a statistical process - you can draw analogy with radioactive decay - nuclei of say Uranium-238 are generally not stable, but only some of them disitegrate at a specific moment. The reason for this is that even if the nuclei is unstable - product of it's decay are lower in energy, then the nuclei itself - then it still requires some energy for it to decay. The same is true for molecules.
It is like as if there was snow on a mountain - it want to move to the Earth's surface, because it is a more favorable position energetically, but for this to happen we first should melt it .