Metagenomic shotgun data with internal control
The problem with correlations in relative scale is know on the literature, it has been suggested to change to other metrics. So I wouldn't use it for internal control. 

As you can see on figure 3 of the linked article the correlation on the absolute scale tend to be higher. So I would say this is within expectations. 

As other way for internal controls are blanks (Just water to see if there are any contaminants), and technical replications, to make sure that the measure is correct not some problem with picking some amplifications instead of others...

Also you don't mention it but the tool and library used to impute the microorganism is also important. You can check with other tools to see if the estimation is similar.