The subject in the sentence "Das Thema der Ausstellung waren die Höhlenmenschen." is actually "die Höhlenmensschen", not "das Thema". The sentence structure here has just changed around. You could also say:
Die Höhlenmenschen waren das Thema der Ausstellung.
It is the same sentence, the sentence units are just ordered in a different way.
Therefore, "waren" is plural because it refers back to "die Höhlenmenschen".
I hope that makes it clearer to you.
Leah von Rocket German