I have a multiple entrance Schengen visa issued from a Spanish embassy. I travelled to Spain, but I had a connecting flight in Frankfurt, so I have a Frankfurt stamp for entry and exit. I have another trip to Germany in a few days. Can I use the same visa although nothing proves that I used my Spanish visa and went to the country of issuance?
The visa is in any case valid, there is nothing that explicitly precludes doing what you did. If the German border guards ask you about it, simply explaining you were in transit should be enough.
If they are suspicious, having some documentation of your trip to Spain (boarding pass from the previous flight if you still have them or anything else that shows you have been to Spain) might help. Entry/exit stamps are not the only things you can use to prove you used the visa as intended.