I got a similar GC content graphic when analyzing the transcriptome of olive roots infected with a fungus.
It turn out that after 7 and 15 days the population of new and opportunistic microorganisms evolved along the infection and changed the GC peaks from a unimodal pike to a composed curve like yours
What I am trying to say is that GC curves can also be compatible with the presence of contaminants.
To answer to this you need to know what percentage of the total reads map to your human sequences. If this is high this is compatible with the presence of a set of very expressed genes. It that percentage drops substantially, you can have an indication of contaminants reads