Without links to, or presentation of, examples of the two formulae it is not possible to be sure that the following explains the particular experience of the poster, but nevertheless I provide it as there has been some interest in the question
The chemical formula depends on the actual molecular structure
This statement may seem obvious, but certain molecules can exist in different states — in biochemistry acids and bases especially can be ionized or not.
If one consults the catalogue of a chemical company, one finds the following diagram of one type of cAMP that they sell in powdered form, in which the phosphate group is shown protonated:
The chemical formulae is given with 12 hydrogens, to reflect this: C10H12N5O6P.
If one consults the Wikipedia entry for cAMP, one is provided with chemical information in the standard form used in Wikipedia, with the phosphate group shown ionized in the diagram of the molecule:
The chemical formulae is given with 11 hydrogens, to reflect this: C10H11N5O6P.
Does it matter?
It matters if you are in the laboratory and preparing a solution of cAMP at a particular concentration. In this case the error would only be about 0.3%, but if it were a salt of an acid, that would have a greater effect. Use the MW written on the label of the bottle.
It matters if you are doing metabolomics and identifying species by their molecular mass, but the species present will depend on how the experiment is done, and one is unlikely to be dealing with this oneself — your software will identify the species for you.
So, in practice, not very much. But in general it matters a lot that one thinks about the ionization state of molecules in solution in biochemistry, and understands how this will vary with the pH.